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/7lkh_23408.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.5 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.pdb" } resolution = 3.5 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= 0.002 sd= 0.021 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 8 5.16 5 C 2645 2.51 5 N 715 2.21 5 O 788 1.98 5 H 4080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 87": "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: 8236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4686 Inner-chain residues flagged as termini: ['pdbres="VAL A 72 "', 'pdbres="ARG A 81 "', 'pdbres="GLU A 278 "', 'pdbres="THR A 637 "'] Classifications: {'peptide': 286} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 22, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1865 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1685 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 1.36, per 1000 atoms: 0.17 Number of scatterers: 8236 At special positions: 0 Unit cell: (71.28, 100.44, 84.24, 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 8 16.00 O 788 8.00 N 715 7.00 C 2645 6.00 H 4080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 1.72 Conformation dependent library (CDL) restraints added in 249.9 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 20.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.618A pdb=" N ARG A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 191 through 198 removed outlier: 5.206A pdb=" N HIS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 650 through 653 Processing helix chain 'A' and resid 656 through 666 removed outlier: 4.479A pdb=" N TRP A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Proline residue: A 660 - end of helix Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 61 through 64 Processing sheet with id= B, first strand: chain 'A' and resid 232 through 240 removed outlier: 6.140A pdb=" N ILE A 681 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS A 99 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 683 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 101 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 685 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.554A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= F, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.271A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 85 through 90 108 hydrogen bonds defined for protein. 267 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: 1.35 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 4079 1.14 - 1.31: 676 1.31 - 1.48: 1790 1.48 - 1.64: 1787 1.64 - 1.81: 9 Bond restraints: 8341 Sorted by residual: bond pdb=" N SER A 661 " pdb=" H SER A 661 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" N LEU H 45 " pdb=" H LEU H 45 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N ASN A 224 " pdb=" H ASN A 224 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N GLN H 39 " pdb=" H GLN H 39 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" N TYR L 50 " pdb=" H TYR L 50 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 8336 not shown) Histogram of bond angle deviations from ideal: 101.10 - 107.70: 670 107.70 - 114.29: 9525 114.29 - 120.88: 2770 120.88 - 127.48: 2017 127.48 - 134.07: 57 Bond angle restraints: 15039 Sorted by residual: angle pdb=" N SER L 52 " pdb=" CA SER L 52 " pdb=" CB SER L 52 " ideal model delta sigma weight residual 114.17 110.90 3.27 1.14e+00 7.69e-01 8.25e+00 angle pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 120.81 118.47 2.34 8.60e-01 1.35e+00 7.42e+00 angle pdb=" C ASP A 83 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.91e+00 angle pdb=" N SER A 117 " pdb=" CA SER A 117 " pdb=" C SER A 117 " ideal model delta sigma weight residual 112.35 109.62 2.73 1.34e+00 5.57e-01 4.14e+00 angle pdb=" N PRO A 155 " pdb=" CA PRO A 155 " pdb=" C PRO A 155 " ideal model delta sigma weight residual 113.47 110.58 2.89 1.43e+00 4.89e-01 4.09e+00 ... (remaining 15034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3641 16.26 - 32.52: 217 32.52 - 48.77: 68 48.77 - 65.03: 28 65.03 - 81.29: 8 Dihedral angle restraints: 3962 sinusoidal: 2137 harmonic: 1825 Sorted by residual: dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 381 0.029 - 0.057: 175 0.057 - 0.086: 32 0.086 - 0.114: 38 0.114 - 0.143: 12 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE A 96 " pdb=" N ILE A 96 " pdb=" C ILE A 96 " pdb=" CB ILE A 96 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL H 93 " pdb=" N VAL H 93 " pdb=" C VAL H 93 " pdb=" CB VAL H 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 635 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 155 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 65 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 66 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 117 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 118 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.018 5.00e-02 4.00e+02 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 389 2.11 - 2.73: 13130 2.73 - 3.35: 22266 3.35 - 3.98: 30686 3.98 - 4.60: 45254 Nonbonded interactions: 111725 Sorted by model distance: nonbonded pdb="HD22 ASN L 34 " pdb=" O TYR L 49 " model vdw 1.483 1.850 nonbonded pdb=" O SER A 117 " pdb=" HG SER A 120 " model vdw 1.538 1.850 nonbonded pdb=" O GLY A 87 " pdb=" HH TYR A 674 " model vdw 1.572 1.850 nonbonded pdb=" OD2 ASP A 188 " pdb=" HG1 THR A 194 " model vdw 1.590 1.850 nonbonded pdb=" OE1 GLN H 5 " pdb=" H GLN H 5 " model vdw 1.620 1.850 ... (remaining 111720 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=0.50 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: 0.020 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: 0.040 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.900 Find NCS groups from input model: 0.050 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:6.260 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.055 4261 Z= 0.157 Angle : 0.554 5.275 5799 Z= 0.303 Chirality : 0.042 0.143 638 Planarity : 0.004 0.052 746 Dihedral : 12.270 81.289 1562 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.13 % Favored : 93.48 % Rotamer: Outliers : 0.43 % Allowed : 1.74 % Favored : 97.83 % 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: -1.47 (0.36), residues: 506 helix: -0.64 (0.55), residues: 73 sheet: -0.68 (0.38), residues: 161 loop : -1.20 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 652 TYR 0.015 0.001 TYR H 99 PHE 0.010 0.001 PHE A 97 TRP 0.007 0.001 TRP A 84 HIS 0.003 0.001 HIS H 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.7973 (mmt90) cc_final: 0.7470 (mmm-85) REVERT: L 4 MET cc_start: 0.8134 (mmm) cc_final: 0.7366 (mmm) REVERT: L 28 ASP cc_start: 0.7632 (p0) cc_final: 0.7334 (p0) outliers start: 2 outliers final: 1 residues processed: 83 average time/residue: 0.1967 time to fit residues: 20.1450 Evaluate side-chains 50 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 198 HIS L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4261 Z= 0.257 Angle : 0.560 5.963 5799 Z= 0.287 Chirality : 0.044 0.147 638 Planarity : 0.005 0.058 746 Dihedral : 6.225 75.960 575 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.30 % Allowed : 7.61 % Favored : 91.09 % 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: -0.93 (0.38), residues: 506 helix: -0.07 (0.61), residues: 73 sheet: -0.44 (0.38), residues: 167 loop : -0.82 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 267 TYR 0.024 0.002 TYR H 99 PHE 0.008 0.001 PHE A 97 TRP 0.009 0.001 TRP A 84 HIS 0.003 0.001 HIS A 697 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.7925 (mmt90) cc_final: 0.7488 (mmm-85) REVERT: L 28 ASP cc_start: 0.7797 (p0) cc_final: 0.7472 (p0) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.3315 time to fit residues: 27.6646 Evaluate side-chains 55 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 ASN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4261 Z= 0.214 Angle : 0.536 5.734 5799 Z= 0.274 Chirality : 0.043 0.147 638 Planarity : 0.005 0.060 746 Dihedral : 5.984 76.480 575 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.52 % Allowed : 9.13 % Favored : 89.35 % 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: -0.72 (0.38), residues: 506 helix: -0.06 (0.60), residues: 73 sheet: -0.28 (0.39), residues: 161 loop : -0.64 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.022 0.002 TYR H 99 PHE 0.009 0.001 PHE A 97 TRP 0.008 0.001 TRP A 84 HIS 0.004 0.001 HIS A 697 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 28 ASP cc_start: 0.8089 (p0) cc_final: 0.7749 (p0) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.2608 time to fit residues: 20.1754 Evaluate side-chains 57 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 ASN L 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4261 Z= 0.249 Angle : 0.558 5.730 5799 Z= 0.287 Chirality : 0.044 0.149 638 Planarity : 0.006 0.074 746 Dihedral : 5.919 74.697 575 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.17 % Allowed : 9.13 % 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: -0.75 (0.38), residues: 506 helix: -0.11 (0.61), residues: 72 sheet: -0.24 (0.39), residues: 163 loop : -0.70 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 13 TYR 0.023 0.002 TYR H 99 PHE 0.010 0.001 PHE A 97 TRP 0.008 0.001 TRP A 84 HIS 0.006 0.001 HIS A 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 28 ASP cc_start: 0.8081 (p0) cc_final: 0.7774 (p0) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.2005 time to fit residues: 14.7928 Evaluate side-chains 56 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 697 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 ASN L 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 4261 Z= 0.140 Angle : 0.500 5.541 5799 Z= 0.254 Chirality : 0.041 0.135 638 Planarity : 0.005 0.056 746 Dihedral : 5.496 70.876 575 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.96 % Allowed : 9.13 % Favored : 88.91 % 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: -0.45 (0.39), residues: 506 helix: 0.22 (0.63), residues: 72 sheet: -0.09 (0.40), residues: 163 loop : -0.49 (0.42), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 267 TYR 0.018 0.001 TYR H 99 PHE 0.007 0.001 PHE A 97 TRP 0.010 0.001 TRP A 84 HIS 0.006 0.001 HIS A 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7248 (mttt) cc_final: 0.6745 (mttt) REVERT: L 28 ASP cc_start: 0.8012 (p0) cc_final: 0.7753 (p0) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.1775 time to fit residues: 12.7855 Evaluate side-chains 58 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 697 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4261 Z= 0.159 Angle : 0.506 5.519 5799 Z= 0.256 Chirality : 0.042 0.144 638 Planarity : 0.006 0.067 746 Dihedral : 5.314 69.872 575 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.96 % Allowed : 9.35 % 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: -0.39 (0.39), residues: 506 helix: 0.33 (0.63), residues: 72 sheet: -0.07 (0.40), residues: 162 loop : -0.45 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 267 TYR 0.019 0.001 TYR H 99 PHE 0.007 0.001 PHE A 97 TRP 0.008 0.001 TRP A 84 HIS 0.007 0.001 HIS A 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 713.27 seconds wall clock time: 12 minutes 43.78 seconds (763.78 seconds total)