Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.3 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.map" } resolution = 3.3 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.095 sd= 0.238 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2087 2.51 5 N 553 2.21 5 O 630 1.98 5 H 3157 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6441 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3007 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1835 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1599 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Time building chain proxies: 1.11, per 1000 atoms: 0.17 Number of scatterers: 6441 At special positions: 0 Unit cell: (67.1, 88, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 630 8.00 N 553 7.00 C 2087 6.00 H 3157 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 235.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 9.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.502A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.333A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'L' and resid 81 through 84 No H-bonds generated for 'chain 'L' and resid 81 through 84' Processing sheet with id= A, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.509A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.754A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= D, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.031A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 114 through 116 removed outlier: 3.583A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.731A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.856A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 98 through 100 removed outlier: 6.369A pdb=" N GLN L 39 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS L 41 " --> pdb=" O PHE L 46 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE L 46 " --> pdb=" O LYS L 41 " (cutoff:3.500A) 81 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3157 1.15 - 1.32: 530 1.32 - 1.49: 1488 1.49 - 1.66: 1334 1.66 - 1.83: 16 Bond restraints: 6525 Sorted by residual: bond pdb=" N ARG A 355 " pdb=" H ARG A 355 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N ASP A 405 " pdb=" H ASP A 405 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N ASN L 55 " pdb=" H ASN L 55 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N CYS H 22 " pdb=" H CYS H 22 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N THR L 21 " pdb=" H THR L 21 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 ... (remaining 6520 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.39: 282 107.39 - 114.07: 7372 114.07 - 120.75: 2255 120.75 - 127.43: 1758 127.43 - 134.10: 39 Bond angle restraints: 11706 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N THR L 53 " pdb=" CA THR L 53 " ideal model delta sigma weight residual 125.66 130.28 -4.62 1.85e+00 2.92e-01 6.23e+00 angle pdb=" CA CYS H 95 " pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " ideal model delta sigma weight residual 114.40 119.71 -5.31 2.30e+00 1.89e-01 5.33e+00 angle pdb=" C ARG A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta sigma weight residual 119.99 122.43 -2.44 1.13e+00 7.83e-01 4.65e+00 angle pdb=" N GLY L 52 " pdb=" CA GLY L 52 " pdb=" C GLY L 52 " ideal model delta sigma weight residual 115.30 112.40 2.90 1.44e+00 4.82e-01 4.05e+00 angle pdb=" C TYR H 94 " pdb=" N CYS H 95 " pdb=" CA CYS H 95 " ideal model delta sigma weight residual 121.42 124.19 -2.77 1.43e+00 4.89e-01 3.76e+00 ... (remaining 11701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 2873 17.73 - 35.46: 199 35.46 - 53.20: 51 53.20 - 70.93: 13 70.93 - 88.66: 4 Dihedral angle restraints: 3140 sinusoidal: 1656 harmonic: 1484 Sorted by residual: dihedral pdb=" CA TRP L 93 " pdb=" C TRP L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 123.27 -30.27 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual 93.00 67.28 25.72 1 1.00e+01 1.00e-02 9.51e+00 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 295 0.031 - 0.061: 129 0.061 - 0.092: 41 0.092 - 0.122: 29 0.122 - 0.153: 4 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE L 77 " pdb=" N ILE L 77 " pdb=" C ILE L 77 " pdb=" CB ILE L 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 495 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 41 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO L 42 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 39 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO H 40 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO H 40 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 40 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.075 9.50e-02 1.11e+02 2.54e-02 9.74e-01 pdb=" NE ARG A 355 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 355 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 355 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 355 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG A 355 " 0.000 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 289 2.07 - 2.70: 9315 2.70 - 3.33: 17483 3.33 - 3.97: 24689 3.97 - 4.60: 35702 Nonbonded interactions: 87478 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" HG1 THR A 523 " model vdw 1.436 1.850 nonbonded pdb=" HZ2 LYS H 64 " pdb=" O SER H 84 " model vdw 1.478 1.850 nonbonded pdb="HH12 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.506 1.850 nonbonded pdb=" O THR H 53 " pdb=" HZ3 LYS H 71 " model vdw 1.515 1.850 nonbonded pdb=" HE1 TRP H 52 " pdb=" OD1 ASN H 58 " model vdw 1.523 1.850 ... (remaining 87473 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.51 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:4.910 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3368 Z= 0.174 Angle : 0.585 5.986 4588 Z= 0.318 Chirality : 0.044 0.153 498 Planarity : 0.004 0.037 593 Dihedral : 11.937 88.662 1181 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.00 % Favored : 93.76 % Rotamer: Outliers : 0.85 % Allowed : 3.94 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.38), residues: 417 helix: -2.37 (0.67), residues: 32 sheet: -0.54 (0.42), residues: 143 loop : -1.19 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.009 0.001 TYR A 423 PHE 0.008 0.001 PHE A 400 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8342 (tt0) cc_final: 0.8138 (tt0) REVERT: H 112 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8049 (pp30) REVERT: L 7 GLU cc_start: 0.6656 (mp0) cc_final: 0.6419 (mp0) outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.1842 time to fit residues: 22.1164 Evaluate side-chains 83 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 39 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3368 Z= 0.269 Angle : 0.573 5.137 4588 Z= 0.303 Chirality : 0.043 0.144 498 Planarity : 0.004 0.038 593 Dihedral : 7.040 44.234 476 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.69 % Allowed : 11.83 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.38), residues: 417 helix: -2.22 (0.72), residues: 32 sheet: -0.26 (0.44), residues: 132 loop : -1.19 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.010 0.001 TYR A 423 PHE 0.009 0.001 PHE A 490 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS L 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7678 (pt0) cc_final: 0.7382 (pt0) REVERT: L 7 GLU cc_start: 0.6814 (mp0) cc_final: 0.6514 (mp0) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.3279 time to fit residues: 33.3626 Evaluate side-chains 80 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 39 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 0.0770 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3368 Z= 0.191 Angle : 0.534 4.815 4588 Z= 0.281 Chirality : 0.042 0.143 498 Planarity : 0.004 0.042 593 Dihedral : 7.033 48.404 476 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.97 % Allowed : 12.68 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.40), residues: 417 helix: -2.20 (0.70), residues: 33 sheet: -0.09 (0.45), residues: 132 loop : -1.02 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 466 TYR 0.009 0.001 TYR A 423 PHE 0.006 0.001 PHE A 490 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS L 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.8453 (m-80) cc_final: 0.7909 (m-80) REVERT: L 7 GLU cc_start: 0.6831 (mp0) cc_final: 0.6281 (mp0) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.2511 time to fit residues: 25.7543 Evaluate side-chains 81 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 0.0070 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN H 3 GLN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3368 Z= 0.182 Angle : 0.520 4.631 4588 Z= 0.271 Chirality : 0.042 0.139 498 Planarity : 0.004 0.056 593 Dihedral : 6.716 52.329 473 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.25 % Allowed : 14.08 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.40), residues: 417 helix: -2.18 (0.71), residues: 33 sheet: -0.11 (0.45), residues: 132 loop : -0.95 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 466 TYR 0.012 0.001 TYR A 365 PHE 0.007 0.001 PHE A 490 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.001 HIS L 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.8445 (m-80) cc_final: 0.7857 (m-80) REVERT: L 7 GLU cc_start: 0.6584 (mp0) cc_final: 0.6218 (mp0) outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.2120 time to fit residues: 22.3923 Evaluate side-chains 85 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN H 3 GLN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3368 Z= 0.227 Angle : 0.524 4.667 4588 Z= 0.276 Chirality : 0.043 0.155 498 Planarity : 0.005 0.062 593 Dihedral : 6.770 53.642 473 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.97 % Allowed : 15.21 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.40), residues: 417 helix: -2.11 (0.72), residues: 33 sheet: -0.16 (0.45), residues: 132 loop : -0.92 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.008 0.001 TYR A 423 PHE 0.008 0.001 PHE A 490 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS L 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8166 (m-30) cc_final: 0.7673 (m-30) REVERT: L 7 GLU cc_start: 0.6696 (mp0) cc_final: 0.6317 (mp0) outliers start: 7 outliers final: 6 residues processed: 87 average time/residue: 0.1584 time to fit residues: 16.5532 Evaluate side-chains 86 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 30.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 3368 Z= 0.151 Angle : 0.513 5.241 4588 Z= 0.264 Chirality : 0.043 0.141 498 Planarity : 0.005 0.066 593 Dihedral : 6.561 55.365 473 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.69 % Allowed : 16.06 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.41), residues: 417 helix: -1.91 (0.77), residues: 33 sheet: -0.02 (0.46), residues: 132 loop : -0.78 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.007 0.001 TYR A 423 PHE 0.006 0.001 PHE A 400 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS L 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 632.55 seconds wall clock time: 11 minutes 19.77 seconds (679.77 seconds total)