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/8idn_35369.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8idn_35369.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.35 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8idn_35369.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8idn_35369.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8idn_35369.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8idn_35369.map" } resolution = 3.35 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= 0.021 sd= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2169 atoms to isotropic. 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 2064 2.51 5 N 540 2.21 5 O 627 1.98 5 H 3125 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3010 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1770 Classifications: {'peptide': 116} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1590 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 1.12, per 1000 atoms: 0.18 Number of scatterers: 6370 At special positions: 0 Unit cell: (69.68, 75.04, 89.11, 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 627 8.00 N 540 7.00 C 2064 6.00 H 3125 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 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 109 " distance=2.04 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: 1.30 Conformation dependent library (CDL) restraints added in 195.2 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 7.9% alpha, 27.4% 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 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.170A 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 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'H' and resid 80 through 82 No H-bonds generated for 'chain 'H' and resid 80 through 82' Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing sheet with id= A, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.709A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= C, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.665A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.056A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.949A pdb=" N LYS L 124 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR L 31 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR L 126 " --> pdb=" O THR L 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 106 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE L 69 " --> pdb=" O TRP L 56 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN L 58 " --> pdb=" O GLY L 67 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLY L 67 " --> pdb=" O GLN L 58 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS L 60 " --> pdb=" O PHE L 65 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE L 65 " --> pdb=" O LYS L 60 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 36 through 42 Processing sheet with id= G, first strand: chain 'L' and resid 111 through 113 removed outlier: 3.763A pdb=" N TYR L 113 " --> pdb=" O HIS L 116 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 207 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: 1.05 Time building geometry restraints manager: 1.50 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: 3125 1.15 - 1.31: 531 1.31 - 1.48: 1421 1.48 - 1.65: 1358 1.65 - 1.82: 16 Bond restraints: 6451 Sorted by residual: bond pdb=" N ALA A 411 " pdb=" H ALA A 411 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.97e+01 bond pdb=" N SER L 86 " pdb=" H SER L 86 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" N LEU L 125 " pdb=" H LEU L 125 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N THR H 42 " pdb=" H THR H 42 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" N CYS A 432 " pdb=" H CYS A 432 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 ... (remaining 6446 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.46: 286 107.46 - 114.11: 7414 114.11 - 120.76: 2115 120.76 - 127.41: 1738 127.41 - 134.07: 38 Bond angle restraints: 11591 Sorted by residual: angle pdb=" CA ASN A 440 " pdb=" C ASN A 440 " pdb=" N LEU A 441 " ideal model delta sigma weight residual 116.84 122.09 -5.25 1.71e+00 3.42e-01 9.41e+00 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 111.45 108.87 2.58 9.30e-01 1.16e+00 7.72e+00 angle pdb=" CA ASN A 440 " pdb=" C ASN A 440 " pdb=" O ASN A 440 " ideal model delta sigma weight residual 120.51 116.94 3.57 1.43e+00 4.89e-01 6.24e+00 angle pdb=" CA GLY L 70 " pdb=" C GLY L 70 " pdb=" N ALA L 71 " ideal model delta sigma weight residual 114.75 117.06 -2.31 1.40e+00 5.10e-01 2.72e+00 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 111.20 113.42 -2.22 1.39e+00 5.18e-01 2.54e+00 ... (remaining 11586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 2791 14.81 - 29.61: 207 29.61 - 44.42: 64 44.42 - 59.23: 32 59.23 - 74.04: 4 Dihedral angle restraints: 3098 sinusoidal: 1639 harmonic: 1459 Sorted by residual: dihedral pdb=" N LYS A 356 " pdb=" CA LYS A 356 " pdb=" CB LYS A 356 " pdb=" CG LYS A 356 " ideal model delta sinusoidal sigma weight residual -60.00 -109.61 49.61 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA TYR H 113 " pdb=" C TYR H 113 " pdb=" N CYS H 114 " pdb=" CA CYS H 114 " ideal model delta harmonic sigma weight residual 180.00 166.08 13.92 0 5.00e+00 4.00e-02 7.75e+00 dihedral pdb=" CA CYS H 41 " pdb=" CB CYS H 41 " pdb=" SG CYS H 41 " pdb=" SG CYS H 114 " ideal model delta sinusoidal sigma weight residual 79.00 125.84 -46.84 1 2.00e+01 2.50e-03 7.58e+00 ... (remaining 3095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 300 0.032 - 0.064: 139 0.064 - 0.096: 34 0.096 - 0.128: 23 0.128 - 0.160: 3 Chirality restraints: 499 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 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA ILE L 106 " pdb=" N ILE L 106 " pdb=" C ILE L 106 " pdb=" CB ILE L 106 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE L 88 " pdb=" N ILE L 88 " pdb=" C ILE L 88 " pdb=" CB ILE L 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 496 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 58 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.33e-01 pdb=" N PRO H 59 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO H 59 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 59 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.013 5.00e-02 4.00e+02 2.02e-02 6.52e-01 pdb=" N PRO A 463 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 400 " -0.008 2.00e-02 2.50e+03 4.42e-03 5.85e-01 pdb=" CG PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 400 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 400 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 400 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 400 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 400 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 400 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 400 " -0.001 2.00e-02 2.50e+03 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 408 2.15 - 2.76: 11052 2.76 - 3.38: 16246 3.38 - 3.99: 22716 3.99 - 4.60: 33243 Nonbonded interactions: 83665 Sorted by model distance: nonbonded pdb=" OE1 GLN A 493 " pdb="HD21 ASN L 73 " model vdw 1.540 1.850 nonbonded pdb=" OD1 ASN A 439 " pdb=" HG SER A 443 " model vdw 1.549 1.850 nonbonded pdb=" OE1 GLU L 104 " pdb=" H GLU L 104 " model vdw 1.584 1.850 nonbonded pdb="HH12 ARG A 408 " pdb=" OD1 ASP H 119 " model vdw 1.598 1.850 nonbonded pdb=" O TYR H 120 " pdb=" HG SER L 74 " model vdw 1.606 1.850 ... (remaining 83660 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:4.810 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 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 : 0.002 0.017 3326 Z= 0.148 Angle : 0.504 5.245 4533 Z= 0.279 Chirality : 0.043 0.160 499 Planarity : 0.003 0.029 585 Dihedral : 11.207 74.036 1166 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.30 % Favored : 93.46 % Rotamer: Outliers : 0.28 % Allowed : 1.98 % Favored : 97.74 % 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: -1.16 (0.39), residues: 413 helix: -2.00 (0.97), residues: 27 sheet: 0.28 (0.42), residues: 146 loop : -1.32 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 116 TYR 0.008 0.001 TYR H 113 PHE 0.013 0.001 PHE A 400 TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.1476 time to fit residues: 13.9164 Evaluate side-chains 61 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3326 Z= 0.276 Angle : 0.510 3.715 4533 Z= 0.273 Chirality : 0.043 0.139 499 Planarity : 0.004 0.029 585 Dihedral : 5.714 63.084 461 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 0.85 % Allowed : 7.91 % Favored : 91.24 % 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: -0.84 (0.40), residues: 413 helix: -1.87 (0.97), residues: 27 sheet: 0.43 (0.42), residues: 146 loop : -1.04 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 82 TYR 0.017 0.002 TYR H 113 PHE 0.011 0.001 PHE A 429 TRP 0.008 0.002 TRP L 112 HIS 0.001 0.001 HIS L 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 355 ARG cc_start: 0.6894 (ttm170) cc_final: 0.6662 (tpp80) REVERT: A 396 TYR cc_start: 0.7285 (m-80) cc_final: 0.7065 (m-10) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.2294 time to fit residues: 17.8161 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3326 Z= 0.273 Angle : 0.511 3.672 4533 Z= 0.274 Chirality : 0.043 0.139 499 Planarity : 0.004 0.030 585 Dihedral : 5.523 62.926 461 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.57 % Favored : 94.19 % Rotamer: Outliers : 1.41 % Allowed : 9.89 % Favored : 88.70 % 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: -0.86 (0.41), residues: 413 helix: -2.06 (0.93), residues: 27 sheet: 0.39 (0.42), residues: 146 loop : -1.02 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.017 0.002 TYR H 113 PHE 0.010 0.001 PHE A 456 TRP 0.009 0.002 TRP L 112 HIS 0.003 0.001 HIS L 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 355 ARG cc_start: 0.6784 (ttm170) cc_final: 0.6517 (tpp80) REVERT: L 59 GLU cc_start: 0.6578 (tp30) cc_final: 0.6356 (tp30) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.1894 time to fit residues: 14.1540 Evaluate side-chains 60 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 73 ASN 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: 3.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3326 Z= 0.202 Angle : 0.471 3.612 4533 Z= 0.251 Chirality : 0.042 0.140 499 Planarity : 0.004 0.029 585 Dihedral : 5.220 59.077 461 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.08 % Favored : 94.67 % Rotamer: Outliers : 1.69 % Allowed : 11.30 % Favored : 87.01 % 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: -0.72 (0.41), residues: 413 helix: -1.89 (0.95), residues: 28 sheet: 0.52 (0.42), residues: 145 loop : -0.93 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.013 0.001 TYR H 113 PHE 0.006 0.001 PHE A 490 TRP 0.007 0.001 TRP L 112 HIS 0.001 0.001 HIS L 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.6616 (ttm170) cc_final: 0.6389 (tpp80) REVERT: L 125 LEU cc_start: 0.8955 (tp) cc_final: 0.8718 (tt) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.1488 time to fit residues: 11.2082 Evaluate side-chains 62 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN H 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3326 Z= 0.137 Angle : 0.446 3.538 4533 Z= 0.237 Chirality : 0.042 0.146 499 Planarity : 0.003 0.030 585 Dihedral : 4.587 48.469 461 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 1.13 % Allowed : 11.30 % Favored : 87.57 % 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: -0.54 (0.41), residues: 413 helix: -1.76 (0.98), residues: 28 sheet: 0.61 (0.42), residues: 145 loop : -0.80 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.009 0.001 TYR A 421 PHE 0.006 0.001 PHE A 490 TRP 0.005 0.001 TRP H 127 HIS 0.002 0.001 HIS L 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 125 LEU cc_start: 0.8919 (tp) cc_final: 0.8694 (tt) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.1105 time to fit residues: 9.0365 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 40.0000 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.0050 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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: 0.7421 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3326 Z= 0.115 Angle : 0.444 3.657 4533 Z= 0.235 Chirality : 0.042 0.152 499 Planarity : 0.004 0.033 585 Dihedral : 4.049 34.347 461 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.63 % Favored : 96.13 % Rotamer: Outliers : 0.28 % Allowed : 12.71 % Favored : 87.01 % 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: -0.34 (0.42), residues: 413 helix: -1.60 (0.98), residues: 28 sheet: 0.81 (0.42), residues: 145 loop : -0.70 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.008 0.001 TYR A 421 PHE 0.008 0.001 PHE L 65 TRP 0.004 0.001 TRP A 436 HIS 0.001 0.000 HIS L 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 636.75 seconds wall clock time: 11 minutes 22.42 seconds (682.42 seconds total)