Starting phenix.real_space_refine on Thu Jun 12 17:54:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qee_18353/06_2025/8qee_18353_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qee_18353/06_2025/8qee_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/cci-nas-00/data/ceres_data/8qee_18353/06_2025/8qee_18353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qee_18353/06_2025/8qee_18353.map" model { file = "/net/cci-nas-00/data/ceres_data/8qee_18353/06_2025/8qee_18353_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qee_18353/06_2025/8qee_18353_trim.cif" } 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. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.77, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 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: 3.56 Conformation dependent library (CDL) restraints added in 1.1 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: 1.08 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: 5.05 Time building geometry restraints manager: 4.29 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: 0.00 - 0.92: 22175 0.92 - 1.84: 2088 1.84 - 2.76: 98 2.76 - 3.68: 163 3.68 - 4.60: 12 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: 6084 23.81 - 47.62: 337 47.62 - 71.42: 102 71.42 - 95.23: 17 95.23 - 119.04: 3 Dihedral angle restraints: 6543 sinusoidal: 3545 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 6540 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 2.450 nonbonded pdb=" O SER A 428 " pdb=" HG SER A 429 " model vdw 1.652 2.450 nonbonded pdb=" O ILE A 633 " pdb=" HG1 THR A 637 " model vdw 1.655 2.450 nonbonded pdb=" HH TYR A 455 " pdb=" O LEU A 488 " model vdw 1.663 2.450 nonbonded pdb=" O ALA A 758 " pdb=" HG1 THR A 762 " model vdw 1.668 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 5.600 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: 0.260 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.770 ------------------------------------------------------------------------------- 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 6906 Z= 0.108 Angle : 0.462 6.303 9403 Z= 0.227 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 4) link_NAG-ASN : angle 2.87730 ( 12) link_BETA1-4 : bond 0.00118 ( 1) link_BETA1-4 : angle 3.21860 ( 3) hydrogen bonds : bond 0.21133 ( 405) hydrogen bonds : angle 7.46558 ( 1173) SS BOND : bond 0.00120 ( 6) SS BOND : angle 0.38470 ( 12) covalent geometry : bond 0.00233 ( 6895) covalent geometry : angle 0.44747 ( 9376) *********************** 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 to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 662 ARG cc_start: 0.7502 (ptp90) cc_final: 0.6713 (ptm160) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 1.9907 time to fit residues: 209.6113 Evaluate side-chains 97 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 21 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 420 ASN A 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126175 restraints weight = 20603.103| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.47 r_work: 0.3357 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6906 Z= 0.150 Angle : 0.552 7.038 9403 Z= 0.299 Chirality : 0.040 0.190 1095 Planarity : 0.004 0.035 1163 Dihedral : 9.302 87.738 1078 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.55 % Allowed : 15.84 % Favored : 81.61 % 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: 2.35 (0.30), residues: 819 helix: 1.68 (0.23), residues: 495 sheet: 1.94 (0.80), residues: 43 loop : 1.53 (0.42), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.003 0.001 HIS A 954 PHE 0.017 0.001 PHE A 505 TYR 0.014 0.001 TYR A 711 ARG 0.004 0.000 ARG A 662 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 4) link_NAG-ASN : angle 2.66259 ( 12) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 1.97128 ( 3) hydrogen bonds : bond 0.06343 ( 405) hydrogen bonds : angle 5.60493 ( 1173) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.41378 ( 12) covalent geometry : bond 0.00298 ( 6895) covalent geometry : angle 0.54286 ( 9376) *********************** 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 101 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1068 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7094 (tt0) outliers start: 19 outliers final: 10 residues processed: 99 average time/residue: 1.9899 time to fit residues: 211.6461 Evaluate side-chains 91 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 45 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.150108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126713 restraints weight = 20652.215| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.47 r_work: 0.3367 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6906 Z= 0.133 Angle : 0.527 6.105 9403 Z= 0.279 Chirality : 0.039 0.195 1095 Planarity : 0.004 0.034 1163 Dihedral : 7.074 58.606 1069 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.42 % Allowed : 15.57 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.30), residues: 819 helix: 1.49 (0.23), residues: 496 sheet: 1.88 (0.76), residues: 42 loop : 1.53 (0.42), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 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 662 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 4) link_NAG-ASN : angle 2.79887 ( 12) link_BETA1-4 : bond 0.00017 ( 1) link_BETA1-4 : angle 1.91678 ( 3) hydrogen bonds : bond 0.05257 ( 405) hydrogen bonds : angle 5.17808 ( 1173) SS BOND : bond 0.00127 ( 6) SS BOND : angle 0.41148 ( 12) covalent geometry : bond 0.00281 ( 6895) covalent geometry : angle 0.51706 ( 9376) *********************** 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 106 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 700 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8114 (t) REVERT: A 1002 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 1068 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6999 (tp30) REVERT: A 1075 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7119 (ttt90) outliers start: 18 outliers final: 7 residues processed: 102 average time/residue: 2.0248 time to fit residues: 221.6857 Evaluate side-chains 96 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1075 ARG Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 33 optimal weight: 2.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN A 865 ASN A 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124635 restraints weight = 20549.838| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.46 r_work: 0.3339 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6906 Z= 0.186 Angle : 0.572 7.371 9403 Z= 0.302 Chirality : 0.041 0.168 1095 Planarity : 0.004 0.037 1163 Dihedral : 6.994 59.833 1066 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.01 % Allowed : 16.24 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.30), residues: 819 helix: 1.29 (0.23), residues: 496 sheet: 1.45 (0.76), residues: 43 loop : 1.34 (0.42), residues: 280 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 0.022 0.002 PHE A 505 TYR 0.015 0.002 TYR A 711 ARG 0.003 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 4) link_NAG-ASN : angle 3.26124 ( 12) link_BETA1-4 : bond 0.00015 ( 1) link_BETA1-4 : angle 2.15402 ( 3) hydrogen bonds : bond 0.05374 ( 405) hydrogen bonds : angle 5.16139 ( 1173) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.49464 ( 12) covalent geometry : bond 0.00417 ( 6895) covalent geometry : angle 0.55876 ( 9376) *********************** 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 to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7021 (t80) cc_final: 0.6561 (t80) REVERT: A 412 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7389 (mp) REVERT: A 1068 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: A 1075 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7245 (ttt90) REVERT: A 1122 GLN cc_start: 0.8080 (tp40) cc_final: 0.7774 (tp-100) outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 2.1202 time to fit residues: 222.4796 Evaluate side-chains 97 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1075 ARG Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.148846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125397 restraints weight = 20666.733| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.46 r_work: 0.3349 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6906 Z= 0.155 Angle : 0.543 6.736 9403 Z= 0.287 Chirality : 0.040 0.183 1095 Planarity : 0.004 0.038 1163 Dihedral : 6.777 59.681 1065 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.95 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 16.51 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.30), residues: 819 helix: 1.29 (0.23), residues: 497 sheet: 1.42 (0.75), residues: 43 loop : 1.35 (0.42), residues: 279 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 0.020 0.001 PHE A 505 TYR 0.014 0.002 TYR A 711 ARG 0.002 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 4) link_NAG-ASN : angle 2.97439 ( 12) link_BETA1-4 : bond 0.00002 ( 1) link_BETA1-4 : angle 2.21032 ( 3) hydrogen bonds : bond 0.04969 ( 405) hydrogen bonds : angle 5.05734 ( 1173) SS BOND : bond 0.00132 ( 6) SS BOND : angle 0.46024 ( 12) covalent geometry : bond 0.00337 ( 6895) covalent geometry : angle 0.53145 ( 9376) *********************** 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 104 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 PHE cc_start: 0.6998 (t80) cc_final: 0.6553 (t80) REVERT: A 412 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7448 (mp) REVERT: A 1068 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: A 1075 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7244 (ttt90) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 2.2658 time to fit residues: 235.6068 Evaluate side-chains 98 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1075 ARG Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.148250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124533 restraints weight = 20747.002| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.47 r_work: 0.3336 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.004 0.038 6906 Z= 0.177 Angle : 0.564 7.428 9403 Z= 0.298 Chirality : 0.040 0.173 1095 Planarity : 0.004 0.039 1163 Dihedral : 6.879 58.964 1064 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.83 % Favored : 98.05 % Rotamer: Outliers : 2.55 % Allowed : 16.51 % 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: 1.75 (0.30), residues: 819 helix: 1.23 (0.23), residues: 497 sheet: 1.35 (0.75), residues: 43 loop : 1.30 (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 0.022 0.002 PHE A 505 TYR 0.014 0.002 TYR A 711 ARG 0.002 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 4) link_NAG-ASN : angle 3.25991 ( 12) link_BETA1-4 : bond 0.00103 ( 1) link_BETA1-4 : angle 2.34816 ( 3) hydrogen bonds : bond 0.05121 ( 405) hydrogen bonds : angle 5.06411 ( 1173) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.49833 ( 12) covalent geometry : bond 0.00396 ( 6895) covalent geometry : angle 0.55068 ( 9376) *********************** 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 106 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 PHE cc_start: 0.6988 (t80) cc_final: 0.6541 (t80) REVERT: A 412 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 1068 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: A 1075 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7289 (ttt90) REVERT: A 1122 GLN cc_start: 0.8118 (tp40) cc_final: 0.7785 (tp-100) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 2.7738 time to fit residues: 300.9964 Evaluate side-chains 102 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1075 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.149729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126106 restraints weight = 20519.458| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.46 r_work: 0.3357 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6906 Z= 0.136 Angle : 0.527 6.535 9403 Z= 0.280 Chirality : 0.039 0.188 1095 Planarity : 0.004 0.039 1163 Dihedral : 6.490 59.088 1062 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.08 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 16.24 % Favored : 81.34 % 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: 1.87 (0.30), residues: 819 helix: 1.33 (0.23), residues: 499 sheet: 1.41 (0.75), residues: 43 loop : 1.34 (0.43), 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 0.019 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.002 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 4) link_NAG-ASN : angle 2.84857 ( 12) link_BETA1-4 : bond 0.00006 ( 1) link_BETA1-4 : angle 2.26792 ( 3) hydrogen bonds : bond 0.04694 ( 405) hydrogen bonds : angle 4.97810 ( 1173) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.41032 ( 12) covalent geometry : bond 0.00294 ( 6895) covalent geometry : angle 0.51609 ( 9376) *********************** 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 108 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.6958 (t80) cc_final: 0.6573 (t80) REVERT: A 412 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7504 (mp) REVERT: A 662 ARG cc_start: 0.7578 (ptp90) cc_final: 0.6728 (ptm160) REVERT: A 1019 PHE cc_start: 0.8092 (m-80) cc_final: 0.7876 (m-80) REVERT: A 1068 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: A 1075 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7232 (ttt90) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 2.7121 time to fit residues: 297.8882 Evaluate side-chains 102 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1075 ARG Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.149783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126228 restraints weight = 20488.990| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.46 r_work: 0.3357 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6906 Z= 0.139 Angle : 0.526 6.582 9403 Z= 0.279 Chirality : 0.039 0.183 1095 Planarity : 0.004 0.064 1163 Dihedral : 6.427 59.364 1062 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.71 % Favored : 98.17 % Rotamer: Outliers : 2.55 % Allowed : 16.11 % Favored : 81.34 % 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: 1.90 (0.30), residues: 819 helix: 1.36 (0.23), residues: 499 sheet: 1.45 (0.75), residues: 43 loop : 1.35 (0.43), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 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 0.010 0.000 ARG A 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 4) link_NAG-ASN : angle 2.87497 ( 12) link_BETA1-4 : bond 0.00052 ( 1) link_BETA1-4 : angle 2.24003 ( 3) hydrogen bonds : bond 0.04662 ( 405) hydrogen bonds : angle 4.94300 ( 1173) SS BOND : bond 0.00123 ( 6) SS BOND : angle 0.40202 ( 12) covalent geometry : bond 0.00305 ( 6895) covalent geometry : angle 0.51523 ( 9376) *********************** 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 111 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.6963 (t80) cc_final: 0.6554 (t80) REVERT: A 412 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7526 (mp) REVERT: A 662 ARG cc_start: 0.7601 (ptp90) cc_final: 0.6727 (ptm160) REVERT: A 1019 PHE cc_start: 0.8089 (m-80) cc_final: 0.7872 (m-80) REVERT: A 1068 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: A 1075 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7182 (ttt90) REVERT: A 1156 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.5377 (m-80) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 2.2723 time to fit residues: 251.9133 Evaluate side-chains 106 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1075 ARG Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1156 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.150095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126759 restraints weight = 20426.357| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.45 r_work: 0.3366 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6906 Z= 0.130 Angle : 0.519 6.279 9403 Z= 0.275 Chirality : 0.039 0.187 1095 Planarity : 0.005 0.092 1163 Dihedral : 6.346 59.532 1062 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.95 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 16.51 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.30), residues: 819 helix: 1.40 (0.23), residues: 499 sheet: 1.53 (0.75), residues: 43 loop : 1.38 (0.43), 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 0.018 0.001 PHE A 505 TYR 0.013 0.001 TYR A 711 ARG 0.015 0.000 ARG A 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 4) link_NAG-ASN : angle 2.74264 ( 12) link_BETA1-4 : bond 0.00005 ( 1) link_BETA1-4 : angle 2.19445 ( 3) hydrogen bonds : bond 0.04534 ( 405) hydrogen bonds : angle 4.91535 ( 1173) SS BOND : bond 0.00115 ( 6) SS BOND : angle 0.38148 ( 12) covalent geometry : bond 0.00283 ( 6895) covalent geometry : angle 0.50891 ( 9376) *********************** 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 107 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.6916 (t80) cc_final: 0.6530 (t80) REVERT: A 412 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7514 (mp) REVERT: A 662 ARG cc_start: 0.7575 (ptp90) cc_final: 0.7322 (tmm-80) REVERT: A 1019 PHE cc_start: 0.8048 (m-80) cc_final: 0.7827 (m-80) REVERT: A 1075 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7182 (ttt90) outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 2.2708 time to fit residues: 244.0223 Evaluate side-chains 102 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1075 ARG Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 29 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.150413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127205 restraints weight = 20472.313| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.44 r_work: 0.3376 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6906 Z= 0.125 Angle : 0.512 6.123 9403 Z= 0.271 Chirality : 0.039 0.188 1095 Planarity : 0.005 0.091 1163 Dihedral : 6.258 59.741 1062 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.95 % Favored : 97.92 % Rotamer: Outliers : 1.88 % Allowed : 16.51 % Favored : 81.61 % 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: 2.02 (0.30), residues: 819 helix: 1.44 (0.23), residues: 499 sheet: 1.61 (0.76), residues: 43 loop : 1.39 (0.43), 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 0.013 0.001 TYR A 711 ARG 0.015 0.000 ARG A 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 4) link_NAG-ASN : angle 2.67979 ( 12) link_BETA1-4 : bond 0.00011 ( 1) link_BETA1-4 : angle 2.14417 ( 3) hydrogen bonds : bond 0.04421 ( 405) hydrogen bonds : angle 4.86403 ( 1173) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.35593 ( 12) covalent geometry : bond 0.00270 ( 6895) covalent geometry : angle 0.50209 ( 9376) ********************** 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 106 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.6890 (t80) cc_final: 0.6523 (t80) REVERT: A 412 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 662 ARG cc_start: 0.7562 (ptp90) cc_final: 0.7338 (tmm-80) REVERT: A 1075 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7199 (ttt90) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 2.3043 time to fit residues: 250.2413 Evaluate side-chains 101 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1075 ARG Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.150689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127583 restraints weight = 20417.106| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.43 r_work: 0.3380 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6906 Z= 0.124 Angle : 0.513 6.076 9403 Z= 0.272 Chirality : 0.039 0.189 1095 Planarity : 0.005 0.088 1163 Dihedral : 6.230 59.938 1062 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.95 % Favored : 97.92 % Rotamer: Outliers : 2.15 % Allowed : 16.78 % 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: 2.05 (0.30), residues: 819 helix: 1.47 (0.23), residues: 499 sheet: 1.61 (0.75), residues: 43 loop : 1.40 (0.43), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.003 0.001 HIS A 954 PHE 0.031 0.001 PHE A 634 TYR 0.013 0.001 TYR A 711 ARG 0.015 0.000 ARG A 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 4) link_NAG-ASN : angle 2.65556 ( 12) link_BETA1-4 : bond 0.00118 ( 1) link_BETA1-4 : angle 2.14028 ( 3) hydrogen bonds : bond 0.04386 ( 405) hydrogen bonds : angle 4.84773 ( 1173) SS BOND : bond 0.00111 ( 6) SS BOND : angle 0.36235 ( 12) covalent geometry : bond 0.00268 ( 6895) covalent geometry : angle 0.50342 ( 9376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10956.18 seconds wall clock time: 191 minutes 13.48 seconds (11473.48 seconds total)