Starting phenix.real_space_refine on Sun Dec 10 07:43:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qee_18353/12_2023/8qee_18353_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qee_18353/12_2023/8qee_18353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qee_18353/12_2023/8qee_18353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qee_18353/12_2023/8qee_18353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qee_18353/12_2023/8qee_18353_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qee_18353/12_2023/8qee_18353_trim.pdb" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.001 sd= 0.066 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 33 5.16 5 C 4411 2.51 5 N 1054 2.21 5 O 1359 1.98 5 H 6889 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 909": "OD1" <-> "OD2" Residue "A PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A GLU 1101": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13746 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 13251 Classifications: {'peptide': 823} Link IDs: {'PTRANS': 34, 'TRANS': 788} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 467 Unusual residues: {'NAG': 3, 'Y01': 1} Classifications: {'undetermined': 4, 'water': 130} Link IDs: {None: 133} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.65, per 1000 atoms: 0.48 Number of scatterers: 13746 At special positions: 0 Unit cell: (74.405, 76.993, 137.811, 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 33 16.00 O 1359 8.00 N 1054 7.00 C 4411 6.00 H 6889 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 868 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 869 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 879 " - pdb=" SG CYS A 888 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1202 " - " ASN A 401 " " NAG A1203 " - " ASN A 940 " " NAG A1204 " - " ASN A 900 " " NAG B 1 " - " ASN A 513 " Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 3 sheets defined 67.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 324 through 337 removed outlier: 4.193A pdb=" N THR A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 360 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.662A pdb=" N ASN A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 Processing helix chain 'A' and resid 557 through 576 Processing helix chain 'A' and resid 584 through 609 removed outlier: 3.731A pdb=" N LEU A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.895A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.624A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 682 Proline residue: A 665 - end of helix Processing helix chain 'A' and resid 686 through 722 removed outlier: 3.764A pdb=" N TYR A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 745 removed outlier: 3.935A pdb=" N TYR A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 767 removed outlier: 3.574A pdb=" N PHE A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.630A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 784 through 797 removed outlier: 4.357A pdb=" N ASP A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 907 through 918 removed outlier: 3.721A pdb=" N MET A 911 " --> pdb=" O GLY A 907 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 916 " --> pdb=" O GLU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 958 through 974 Processing helix chain 'A' and resid 987 through 995 removed outlier: 4.002A pdb=" N VAL A 992 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN A 993 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 994 " --> pdb=" O PHE A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1021 Processing helix chain 'A' and resid 1022 through 1048 Processing helix chain 'A' and resid 1052 through 1079 removed outlier: 3.505A pdb=" N GLY A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1099 through 1107 Processing helix chain 'A' and resid 1107 through 1117 removed outlier: 4.708A pdb=" N VAL A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1121 Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'A' and resid 1130 through 1147 Processing helix chain 'A' and resid 1147 through 1155 Processing sheet with id=AA1, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AA2, first strand: chain 'A' and resid 937 through 939 removed outlier: 4.311A pdb=" N ASP A 980 " --> pdb=" O LYS A 808 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 870 through 872 405 hydrogen bonds defined for protein. 1173 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: 5.55 Time building geometry restraints manager: 13.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6882 1.03 - 1.23: 63 1.23 - 1.43: 2859 1.43 - 1.62: 3933 1.62 - 1.82: 47 Bond restraints: 13784 Sorted by residual: bond pdb=" C1 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" N ALA A 324 " pdb=" CA ALA A 324 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ALA A 324 " pdb=" H ALA A 324 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG A1204 " pdb=" O5 NAG A1204 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" C1 NAG A1203 " pdb=" O5 NAG A1203 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 13779 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 358 106.98 - 113.74: 15856 113.74 - 120.49: 4807 120.49 - 127.25: 3448 127.25 - 134.01: 67 Bond angle restraints: 24536 Sorted by residual: angle pdb=" N SER A 429 " pdb=" CA SER A 429 " pdb=" C SER A 429 " ideal model delta sigma weight residual 110.80 106.47 4.33 2.13e+00 2.20e-01 4.14e+00 angle pdb=" N GLU A 430 " pdb=" CA GLU A 430 " pdb=" C GLU A 430 " ideal model delta sigma weight residual 113.72 110.91 2.81 1.52e+00 4.33e-01 3.42e+00 angle pdb=" CB GLN A 893 " pdb=" CG GLN A 893 " pdb=" CD GLN A 893 " ideal model delta sigma weight residual 112.60 115.37 -2.77 1.70e+00 3.46e-01 2.65e+00 angle pdb=" C5 NAG B 1 " pdb=" C4 NAG B 1 " pdb=" O4 NAG B 1 " ideal model delta sigma weight residual 111.70 107.10 4.60 3.00e+00 1.11e-01 2.35e+00 angle pdb=" CA ALA A 324 " pdb=" N ALA A 324 " pdb=" H ALA A 324 " ideal model delta sigma weight residual 114.00 109.46 4.54 3.00e+00 1.11e-01 2.29e+00 ... (remaining 24531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 6021 23.81 - 47.62: 320 47.62 - 71.42: 69 71.42 - 95.23: 17 95.23 - 119.04: 3 Dihedral angle restraints: 6430 sinusoidal: 3432 harmonic: 2998 Sorted by residual: dihedral pdb=" CA SER A 428 " pdb=" C SER A 428 " pdb=" N SER A 429 " pdb=" CA SER A 429 " ideal model delta harmonic sigma weight residual 180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS A 822 " pdb=" SG CYS A 822 " pdb=" SG CYS A 828 " pdb=" CB CYS A 828 " ideal model delta sinusoidal sigma weight residual -86.00 -120.43 34.43 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CA SER A 429 " pdb=" C SER A 429 " pdb=" N GLU A 430 " pdb=" CA GLU A 430 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 6427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1010 0.071 - 0.141: 84 0.141 - 0.212: 0 0.212 - 0.282: 0 0.282 - 0.353: 1 Chirality restraints: 1095 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA VAL A 944 " pdb=" N VAL A 944 " pdb=" C VAL A 944 " pdb=" CB VAL A 944 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE A 449 " pdb=" N ILE A 449 " pdb=" C ILE A 449 " pdb=" CB ILE A 449 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1092 not shown) Planarity restraints: 1954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 931 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.72e+00 pdb=" N PRO A 932 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 932 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 932 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 985 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO A 986 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 998 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 999 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 999 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 999 " 0.015 5.00e-02 4.00e+02 ... (remaining 1951 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1682 2.24 - 2.83: 31066 2.83 - 3.42: 39699 3.42 - 4.01: 56055 4.01 - 4.60: 83492 Nonbonded interactions: 211994 Sorted by model distance: nonbonded pdb=" OD2 ASP A 653 " pdb=" HZ1 LYS A 720 " model vdw 1.652 1.850 nonbonded pdb=" O SER A 428 " pdb=" HG SER A 429 " model vdw 1.652 1.850 nonbonded pdb=" O ILE A 633 " pdb=" HG1 THR A 637 " model vdw 1.655 1.850 nonbonded pdb=" HH TYR A 455 " pdb=" O LEU A 488 " model vdw 1.663 1.850 nonbonded pdb=" O ALA A 758 " pdb=" HG1 THR A 762 " model vdw 1.668 1.850 ... (remaining 211989 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: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.960 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: 0.210 Extract box with map and model: 17.860 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 49.190 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.041 6895 Z= 0.149 Angle : 0.447 4.598 9376 Z= 0.224 Chirality : 0.038 0.353 1095 Planarity : 0.003 0.033 1163 Dihedral : 17.851 119.040 2609 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.15 % Allowed : 17.05 % Favored : 80.81 % 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: 2.41 (0.31), residues: 819 helix: 1.73 (0.24), residues: 486 sheet: 2.21 (0.89), residues: 42 loop : 1.53 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 897 HIS 0.004 0.001 HIS A 954 PHE 0.008 0.001 PHE A 505 TYR 0.007 0.001 TYR A 984 ARG 0.001 0.000 ARG A1075 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.093 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 1.9508 time to fit residues: 206.2234 Evaluate side-chains 96 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.4662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 643 ASN A 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6895 Z= 0.223 Angle : 0.552 7.091 9376 Z= 0.301 Chirality : 0.041 0.215 1095 Planarity : 0.004 0.035 1163 Dihedral : 8.281 88.225 1057 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.36 % Allowed : 16.11 % Favored : 80.54 % 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: 2.29 (0.30), residues: 819 helix: 1.62 (0.23), residues: 495 sheet: 1.97 (0.81), residues: 43 loop : 1.53 (0.42), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.002 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.002 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 1.100 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 104 average time/residue: 1.9576 time to fit residues: 219.7421 Evaluate side-chains 97 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1531 time to fit residues: 2.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN A 691 ASN A 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6895 Z= 0.201 Angle : 0.527 6.186 9376 Z= 0.281 Chirality : 0.040 0.199 1095 Planarity : 0.004 0.036 1163 Dihedral : 6.281 57.455 1057 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.09 % Allowed : 15.84 % Favored : 81.07 % 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: 2.07 (0.30), residues: 819 helix: 1.46 (0.23), residues: 495 sheet: 1.81 (0.79), residues: 43 loop : 1.42 (0.42), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.020 0.001 PHE A 634 TYR 0.013 0.001 TYR A 711 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 1.100 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 2.0904 time to fit residues: 229.2802 Evaluate side-chains 94 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.4424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 ASN A 954 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6895 Z= 0.189 Angle : 0.513 5.906 9376 Z= 0.275 Chirality : 0.039 0.205 1095 Planarity : 0.004 0.037 1163 Dihedral : 6.137 56.564 1057 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.55 % Allowed : 16.64 % Favored : 80.81 % 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: 2.05 (0.30), residues: 819 helix: 1.43 (0.23), residues: 497 sheet: 1.80 (0.78), residues: 43 loop : 1.44 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.002 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 1.9867 time to fit residues: 211.3137 Evaluate side-chains 99 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.2803 time to fit residues: 2.2051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6895 Z= 0.200 Angle : 0.515 5.850 9376 Z= 0.276 Chirality : 0.039 0.201 1095 Planarity : 0.004 0.037 1163 Dihedral : 5.981 50.576 1057 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.59 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 16.64 % Favored : 80.94 % 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: 2.06 (0.30), residues: 819 helix: 1.44 (0.23), residues: 499 sheet: 1.74 (0.78), residues: 43 loop : 1.45 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.019 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.001 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.014 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 99 average time/residue: 2.0413 time to fit residues: 216.9123 Evaluate side-chains 98 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.3687 time to fit residues: 1.8511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6895 Z= 0.224 Angle : 0.524 5.903 9376 Z= 0.281 Chirality : 0.040 0.201 1095 Planarity : 0.004 0.037 1163 Dihedral : 5.961 41.426 1057 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.59 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 17.05 % Favored : 80.54 % 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: 2.04 (0.30), residues: 819 helix: 1.45 (0.23), residues: 497 sheet: 1.70 (0.77), residues: 43 loop : 1.39 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.019 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.105 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 2.1175 time to fit residues: 234.3940 Evaluate side-chains 100 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.3920 time to fit residues: 1.9239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6895 Z= 0.183 Angle : 0.507 5.493 9376 Z= 0.272 Chirality : 0.039 0.202 1095 Planarity : 0.005 0.095 1163 Dihedral : 5.791 41.178 1057 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.71 % Favored : 98.17 % Rotamer: Outliers : 2.55 % Allowed : 16.91 % Favored : 80.54 % 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: 2.11 (0.30), residues: 819 helix: 1.50 (0.23), residues: 499 sheet: 1.77 (0.77), residues: 43 loop : 1.44 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.001 PHE A 505 TYR 0.012 0.001 TYR A 711 ARG 0.015 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.158 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 2.1687 time to fit residues: 232.7198 Evaluate side-chains 101 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.3801 time to fit residues: 1.9208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6895 Z= 0.224 Angle : 0.524 5.655 9376 Z= 0.281 Chirality : 0.040 0.198 1095 Planarity : 0.005 0.082 1163 Dihedral : 5.879 44.025 1057 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.71 % Favored : 98.17 % Rotamer: Outliers : 2.68 % Allowed : 16.78 % Favored : 80.54 % 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: 2.03 (0.30), residues: 819 helix: 1.45 (0.23), residues: 499 sheet: 1.70 (0.77), residues: 43 loop : 1.39 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.020 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.014 0.001 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 1.091 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 106 average time/residue: 2.1792 time to fit residues: 247.1389 Evaluate side-chains 101 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 1.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6895 Z= 0.198 Angle : 0.513 5.346 9376 Z= 0.275 Chirality : 0.039 0.199 1095 Planarity : 0.005 0.077 1163 Dihedral : 5.786 46.955 1057 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.71 % Favored : 98.17 % Rotamer: Outliers : 2.68 % Allowed : 16.91 % Favored : 80.40 % 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: 2.08 (0.30), residues: 819 helix: 1.49 (0.23), residues: 499 sheet: 1.73 (0.77), residues: 43 loop : 1.40 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.012 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.932 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 2.0195 time to fit residues: 225.2783 Evaluate side-chains 102 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.3448 time to fit residues: 1.8591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6895 Z= 0.176 Angle : 0.502 5.047 9376 Z= 0.269 Chirality : 0.039 0.202 1095 Planarity : 0.005 0.096 1163 Dihedral : 5.660 47.787 1057 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.71 % Favored : 98.17 % Rotamer: Outliers : 2.28 % Allowed : 17.05 % Favored : 80.67 % 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: 2.17 (0.30), residues: 819 helix: 1.57 (0.23), residues: 499 sheet: 1.81 (0.77), residues: 43 loop : 1.42 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.003 0.001 HIS A 954 PHE 0.017 0.001 PHE A 505 TYR 0.012 0.001 TYR A 711 ARG 0.017 0.000 ARG A 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.994 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 2.0936 time to fit residues: 231.4906 Evaluate side-chains 100 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 1.4220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126938 restraints weight = 20529.071| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.46 r_work: 0.3367 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6895 Z= 0.171 Angle : 0.496 4.960 9376 Z= 0.266 Chirality : 0.039 0.201 1095 Planarity : 0.005 0.090 1163 Dihedral : 5.590 48.505 1057 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.71 % Favored : 98.17 % Rotamer: Outliers : 2.42 % Allowed : 17.05 % Favored : 80.54 % 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: 2.22 (0.30), residues: 819 helix: 1.59 (0.23), residues: 500 sheet: 1.90 (0.77), residues: 43 loop : 1.45 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.003 0.001 HIS A 954 PHE 0.016 0.001 PHE A 505 TYR 0.012 0.001 TYR A 711 ARG 0.016 0.000 ARG A 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5732.79 seconds wall clock time: 102 minutes 22.23 seconds (6142.23 seconds total)