Starting phenix.real_space_refine on Sun Aug 4 04:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5v_44226/08_2024/9b5v_44226.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5v_44226/08_2024/9b5v_44226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5v_44226/08_2024/9b5v_44226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5v_44226/08_2024/9b5v_44226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5v_44226/08_2024/9b5v_44226.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5v_44226/08_2024/9b5v_44226.cif" } resolution = 3.94 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= 0.000 sd= 0.040 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6074 2.51 5 N 1573 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9527 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.98, per 1000 atoms: 0.63 Number of scatterers: 9527 At special positions: 0 Unit cell: (91.504, 100.016, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1833 8.00 N 1573 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.93 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 46.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.063A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.936A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.887A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.510A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.707A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.796A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.428A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.727A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.565A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.875A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.627A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.625A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.562A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.515A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.521A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.996A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.626A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.671A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.939A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.046A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.046A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.518A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 907 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.321A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.321A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.332A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 removed outlier: 8.804A pdb=" N LEU D 67 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 4 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU D 69 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS D 6 " --> pdb=" O LEU D 69 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1272 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: 3.47 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1616 1.27 - 1.40: 2291 1.40 - 1.54: 5657 1.54 - 1.67: 110 1.67 - 1.81: 64 Bond restraints: 9738 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" C SER A 589 " pdb=" N PHE A 590 " ideal model delta sigma weight residual 1.339 1.277 0.062 5.57e-02 3.22e+02 1.25e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.20e-02 6.94e+03 9.88e-01 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 8.68e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 100.30 - 116.21: 6584 116.21 - 132.12: 6599 132.12 - 148.02: 11 148.02 - 163.93: 0 163.93 - 179.84: 1 Bond angle restraints: 13195 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 127.93 -6.23 1.80e+00 3.09e-01 1.20e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.32 3.21 1.18e+00 7.24e-01 7.47e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.91 4.28 1.76e+00 3.23e-01 5.92e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 103.84 6.74 2.79e+00 1.28e-01 5.83e+00 angle pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.06 106.03 5.03 2.50e+00 1.60e-01 4.05e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 5695 18.05 - 36.10: 188 36.10 - 54.15: 42 54.15 - 72.21: 1 72.21 - 90.26: 3 Dihedral angle restraints: 5929 sinusoidal: 2424 harmonic: 3505 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -176.26 90.26 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB ARG D 74 " pdb=" CG ARG D 74 " pdb=" CD ARG D 74 " pdb=" NE ARG D 74 " ideal model delta sinusoidal sigma weight residual -60.00 -114.00 54.00 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" N GLU A 869 " pdb=" CA GLU A 869 " pdb=" CB GLU A 869 " pdb=" CG GLU A 869 " ideal model delta sinusoidal sigma weight residual -60.00 -113.49 53.49 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1274 0.054 - 0.108: 160 0.108 - 0.161: 34 0.161 - 0.215: 1 0.215 - 0.269: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.88 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.71 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 67 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C LEU D 67 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU D 67 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS D 68 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO C 121 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 60 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.69e-01 pdb=" N PRO C 61 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.012 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 108 2.56 - 3.14: 7921 3.14 - 3.73: 14486 3.73 - 4.31: 20176 4.31 - 4.90: 34385 Nonbonded interactions: 77076 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 1.969 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.020 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.020 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.102 2.170 nonbonded pdb=" OE2 GLU A 468 " pdb="MG MG A1102 " model vdw 2.137 2.170 ... (remaining 77071 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 group one per residue 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: 3.620 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.270 Process input model: 29.620 Find NCS groups from input model: 0.090 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9738 Z= 0.204 Angle : 0.511 6.744 13195 Z= 0.268 Chirality : 0.040 0.269 1471 Planarity : 0.003 0.027 1707 Dihedral : 9.567 80.529 3662 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.83 % Favored : 98.00 % Rotamer: Outliers : 2.36 % Allowed : 2.54 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.41 (0.25), residues: 1199 helix: 1.95 (0.25), residues: 476 sheet: 0.28 (0.37), residues: 217 loop : 0.37 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 702 HIS 0.004 0.001 HIS D 68 PHE 0.009 0.001 PHE A 842 TYR 0.009 0.001 TYR C 134 ARG 0.002 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 CYS cc_start: 0.9489 (m) cc_final: 0.9288 (m) REVERT: A 162 ILE cc_start: 0.9638 (mt) cc_final: 0.9426 (mm) REVERT: A 235 TYR cc_start: 0.8418 (m-80) cc_final: 0.8048 (m-10) REVERT: A 345 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8892 (mm-30) REVERT: A 353 ASP cc_start: 0.8282 (t0) cc_final: 0.7796 (m-30) REVERT: A 357 MET cc_start: 0.8930 (mmm) cc_final: 0.8714 (mmm) REVERT: A 445 ASN cc_start: 0.9149 (m-40) cc_final: 0.8497 (m-40) REVERT: A 448 MET cc_start: 0.9487 (mmp) cc_final: 0.9212 (mmm) REVERT: A 526 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8668 (t80) REVERT: A 557 LEU cc_start: 0.9055 (mt) cc_final: 0.8851 (mp) REVERT: A 562 LEU cc_start: 0.9130 (tp) cc_final: 0.8729 (pp) REVERT: A 606 ILE cc_start: 0.9407 (mt) cc_final: 0.9140 (mm) REVERT: A 622 ASP cc_start: 0.9196 (m-30) cc_final: 0.8778 (t0) REVERT: A 919 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6914 (ptp-170) REVERT: A 955 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.8897 (m-40) REVERT: C 28 ASP cc_start: 0.8386 (m-30) cc_final: 0.8174 (t70) REVERT: C 67 VAL cc_start: 0.9346 (t) cc_final: 0.9115 (t) REVERT: C 88 ILE cc_start: 0.9083 (pt) cc_final: 0.8615 (mp) REVERT: D 50 LEU cc_start: 0.8222 (mt) cc_final: 0.7606 (mt) outliers start: 25 outliers final: 6 residues processed: 197 average time/residue: 0.2599 time to fit residues: 67.9577 Evaluate side-chains 87 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 955 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9738 Z= 0.200 Angle : 0.604 9.309 13195 Z= 0.309 Chirality : 0.044 0.207 1471 Planarity : 0.004 0.055 1707 Dihedral : 5.716 60.553 1341 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.51 % Allowed : 8.01 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.50 (0.25), residues: 1199 helix: 1.87 (0.24), residues: 497 sheet: 0.75 (0.39), residues: 194 loop : 0.33 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 33 HIS 0.004 0.001 HIS D 68 PHE 0.013 0.001 PHE A 237 TYR 0.020 0.001 TYR A 25 ARG 0.006 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8703 (ppp) REVERT: A 235 TYR cc_start: 0.8288 (m-80) cc_final: 0.8019 (m-10) REVERT: A 253 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 285 MET cc_start: 0.8726 (pmm) cc_final: 0.8095 (mpp) REVERT: A 345 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8899 (mm-30) REVERT: A 353 ASP cc_start: 0.8195 (t0) cc_final: 0.7804 (m-30) REVERT: A 357 MET cc_start: 0.9047 (mmm) cc_final: 0.8829 (mmm) REVERT: A 445 ASN cc_start: 0.9142 (m-40) cc_final: 0.8578 (m-40) REVERT: A 464 MET cc_start: 0.8769 (pmt) cc_final: 0.8198 (pmt) REVERT: A 526 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8547 (t80) REVERT: A 562 LEU cc_start: 0.9156 (tp) cc_final: 0.8915 (tp) REVERT: A 605 THR cc_start: 0.9420 (p) cc_final: 0.9194 (t) REVERT: A 622 ASP cc_start: 0.9493 (m-30) cc_final: 0.8767 (t0) REVERT: A 626 MET cc_start: 0.9208 (mmp) cc_final: 0.8800 (mmp) REVERT: A 707 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7595 (mtt180) REVERT: A 809 GLU cc_start: 0.8583 (mp0) cc_final: 0.8233 (tp30) REVERT: A 869 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8746 (mm-30) REVERT: A 906 MET cc_start: 0.7495 (tmm) cc_final: 0.7249 (tmm) REVERT: C 38 MET cc_start: 0.7507 (mmm) cc_final: 0.6666 (mmm) REVERT: C 63 LYS cc_start: 0.9752 (OUTLIER) cc_final: 0.9550 (tppt) REVERT: C 130 ASP cc_start: 0.8601 (t0) cc_final: 0.8211 (p0) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 0.2263 time to fit residues: 32.0839 Evaluate side-chains 79 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9738 Z= 0.188 Angle : 0.557 9.172 13195 Z= 0.279 Chirality : 0.042 0.186 1471 Planarity : 0.004 0.051 1707 Dihedral : 5.366 58.916 1330 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.07 % Allowed : 8.58 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1199 helix: 1.92 (0.24), residues: 499 sheet: 0.72 (0.37), residues: 212 loop : 0.45 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 33 HIS 0.003 0.001 HIS D 68 PHE 0.012 0.001 PHE A 934 TYR 0.011 0.001 TYR A 25 ARG 0.011 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8732 (ppp) REVERT: A 184 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7868 (tpt) REVERT: A 235 TYR cc_start: 0.8343 (m-80) cc_final: 0.8079 (m-10) REVERT: A 285 MET cc_start: 0.8765 (pmm) cc_final: 0.8130 (mpp) REVERT: A 353 ASP cc_start: 0.8339 (t0) cc_final: 0.7839 (m-30) REVERT: A 445 ASN cc_start: 0.9088 (m-40) cc_final: 0.8569 (m-40) REVERT: A 464 MET cc_start: 0.8760 (pmt) cc_final: 0.8236 (pmt) REVERT: A 526 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.8453 (t80) REVERT: A 562 LEU cc_start: 0.9151 (tp) cc_final: 0.8919 (tp) REVERT: A 622 ASP cc_start: 0.9475 (m-30) cc_final: 0.8752 (t0) REVERT: A 626 MET cc_start: 0.9340 (mmp) cc_final: 0.8776 (mmp) REVERT: A 707 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7584 (mtt90) REVERT: A 906 MET cc_start: 0.7516 (tmm) cc_final: 0.7154 (tmm) REVERT: A 945 LEU cc_start: 0.9572 (mt) cc_final: 0.9264 (mt) REVERT: C 7 ASN cc_start: 0.8866 (m110) cc_final: 0.8556 (m110) REVERT: C 52 LEU cc_start: 0.9091 (mp) cc_final: 0.8818 (mt) REVERT: C 63 LYS cc_start: 0.9755 (OUTLIER) cc_final: 0.9548 (tppt) REVERT: C 130 ASP cc_start: 0.8623 (t0) cc_final: 0.8305 (p0) REVERT: D 1 MET cc_start: 0.4357 (tmm) cc_final: 0.3338 (tmm) REVERT: D 50 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7690 (mp) outliers start: 22 outliers final: 11 residues processed: 86 average time/residue: 0.2147 time to fit residues: 27.0091 Evaluate side-chains 80 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9738 Z= 0.188 Angle : 0.534 8.482 13195 Z= 0.268 Chirality : 0.041 0.193 1471 Planarity : 0.003 0.044 1707 Dihedral : 5.202 57.549 1329 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.54 % Allowed : 8.20 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.70 (0.26), residues: 1199 helix: 1.95 (0.24), residues: 499 sheet: 0.70 (0.37), residues: 212 loop : 0.60 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 33 HIS 0.002 0.001 HIS A 604 PHE 0.010 0.001 PHE A 934 TYR 0.009 0.001 TYR A 627 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8816 (p) REVERT: A 218 MET cc_start: 0.5002 (mmm) cc_final: 0.4401 (mmm) REVERT: A 235 TYR cc_start: 0.8361 (m-80) cc_final: 0.8057 (m-10) REVERT: A 285 MET cc_start: 0.8810 (pmm) cc_final: 0.8089 (mpp) REVERT: A 345 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8845 (mm-30) REVERT: A 353 ASP cc_start: 0.8391 (t0) cc_final: 0.7776 (m-30) REVERT: A 445 ASN cc_start: 0.9118 (m-40) cc_final: 0.8592 (m-40) REVERT: A 464 MET cc_start: 0.8763 (pmt) cc_final: 0.8228 (pmt) REVERT: A 526 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8413 (t80) REVERT: A 562 LEU cc_start: 0.9177 (tp) cc_final: 0.8920 (tp) REVERT: A 622 ASP cc_start: 0.9479 (m-30) cc_final: 0.8769 (t0) REVERT: A 626 MET cc_start: 0.9336 (mmp) cc_final: 0.8792 (mmp) REVERT: A 707 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7746 (mtt180) REVERT: A 869 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8828 (mm-30) REVERT: A 906 MET cc_start: 0.7466 (tmm) cc_final: 0.7109 (tmm) REVERT: C 52 LEU cc_start: 0.9135 (mp) cc_final: 0.8881 (mt) REVERT: C 63 LYS cc_start: 0.9763 (OUTLIER) cc_final: 0.9558 (tppt) REVERT: D 1 MET cc_start: 0.4395 (tmm) cc_final: 0.3985 (tmm) outliers start: 27 outliers final: 15 residues processed: 91 average time/residue: 0.1994 time to fit residues: 27.4932 Evaluate side-chains 79 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9738 Z= 0.157 Angle : 0.537 8.296 13195 Z= 0.270 Chirality : 0.042 0.260 1471 Planarity : 0.003 0.052 1707 Dihedral : 5.087 59.541 1329 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.07 % Allowed : 9.52 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.71 (0.26), residues: 1199 helix: 1.98 (0.24), residues: 501 sheet: 0.71 (0.37), residues: 218 loop : 0.57 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 33 HIS 0.002 0.000 HIS D 68 PHE 0.013 0.001 PHE A 934 TYR 0.008 0.001 TYR A 627 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8751 (ppp) REVERT: A 112 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8825 (p) REVERT: A 218 MET cc_start: 0.4289 (mmm) cc_final: 0.3573 (mmm) REVERT: A 235 TYR cc_start: 0.8326 (m-80) cc_final: 0.8040 (m-10) REVERT: A 285 MET cc_start: 0.8788 (pmm) cc_final: 0.8419 (pmm) REVERT: A 345 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8826 (mm-30) REVERT: A 353 ASP cc_start: 0.8392 (t0) cc_final: 0.7765 (m-30) REVERT: A 445 ASN cc_start: 0.9118 (m-40) cc_final: 0.8588 (m-40) REVERT: A 464 MET cc_start: 0.8818 (pmt) cc_final: 0.8293 (pmt) REVERT: A 526 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8353 (t80) REVERT: A 562 LEU cc_start: 0.9169 (tp) cc_final: 0.8934 (tp) REVERT: A 622 ASP cc_start: 0.9488 (m-30) cc_final: 0.8757 (t0) REVERT: A 626 MET cc_start: 0.9348 (mmp) cc_final: 0.8847 (mmp) REVERT: A 707 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7775 (mtt180) REVERT: A 869 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8779 (mm-30) REVERT: A 906 MET cc_start: 0.7454 (tmm) cc_final: 0.7215 (tmm) REVERT: A 908 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8121 (p) REVERT: C 52 LEU cc_start: 0.9163 (mp) cc_final: 0.8958 (mt) REVERT: C 63 LYS cc_start: 0.9759 (OUTLIER) cc_final: 0.9554 (tppt) REVERT: D 1 MET cc_start: 0.4651 (tmm) cc_final: 0.4267 (tmm) outliers start: 22 outliers final: 12 residues processed: 87 average time/residue: 0.2106 time to fit residues: 26.9626 Evaluate side-chains 79 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9738 Z= 0.203 Angle : 0.538 9.583 13195 Z= 0.273 Chirality : 0.042 0.221 1471 Planarity : 0.004 0.053 1707 Dihedral : 5.032 59.555 1329 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.64 % Allowed : 9.71 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.72 (0.26), residues: 1199 helix: 2.06 (0.24), residues: 501 sheet: 0.63 (0.37), residues: 216 loop : 0.54 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 33 HIS 0.002 0.001 HIS A 458 PHE 0.010 0.001 PHE A 985 TYR 0.009 0.001 TYR A 627 ARG 0.002 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 67 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 196 MET cc_start: 0.6054 (mmm) cc_final: 0.5789 (mmm) REVERT: A 218 MET cc_start: 0.4183 (mmm) cc_final: 0.3390 (mmm) REVERT: A 235 TYR cc_start: 0.8359 (m-80) cc_final: 0.8045 (m-10) REVERT: A 285 MET cc_start: 0.8802 (pmm) cc_final: 0.8396 (pmm) REVERT: A 345 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8822 (mm-30) REVERT: A 353 ASP cc_start: 0.8463 (t0) cc_final: 0.7835 (m-30) REVERT: A 445 ASN cc_start: 0.9118 (m-40) cc_final: 0.8578 (m-40) REVERT: A 464 MET cc_start: 0.8820 (pmt) cc_final: 0.8287 (pmt) REVERT: A 526 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 562 LEU cc_start: 0.9142 (tp) cc_final: 0.8873 (tp) REVERT: A 618 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8178 (tppt) REVERT: A 622 ASP cc_start: 0.9479 (m-30) cc_final: 0.8785 (t0) REVERT: A 626 MET cc_start: 0.9333 (mmp) cc_final: 0.8856 (mmp) REVERT: A 707 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7819 (mtt180) REVERT: A 906 MET cc_start: 0.7520 (tmm) cc_final: 0.7185 (tmm) REVERT: C 63 LYS cc_start: 0.9763 (OUTLIER) cc_final: 0.9562 (tppt) REVERT: D 1 MET cc_start: 0.4900 (tmm) cc_final: 0.4279 (tmm) outliers start: 28 outliers final: 15 residues processed: 87 average time/residue: 0.1953 time to fit residues: 25.1815 Evaluate side-chains 78 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9738 Z= 0.163 Angle : 0.542 10.692 13195 Z= 0.270 Chirality : 0.042 0.247 1471 Planarity : 0.003 0.052 1707 Dihedral : 4.984 59.053 1329 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 10.37 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.71 (0.26), residues: 1199 helix: 2.03 (0.24), residues: 502 sheet: 0.60 (0.37), residues: 216 loop : 0.57 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 33 HIS 0.002 0.000 HIS A 305 PHE 0.013 0.001 PHE C 69 TYR 0.010 0.001 TYR D 59 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8831 (p) REVERT: A 235 TYR cc_start: 0.8314 (m-80) cc_final: 0.7992 (m-10) REVERT: A 285 MET cc_start: 0.8806 (pmm) cc_final: 0.8389 (pmm) REVERT: A 345 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8846 (mm-30) REVERT: A 353 ASP cc_start: 0.8456 (t0) cc_final: 0.7833 (m-30) REVERT: A 445 ASN cc_start: 0.9107 (m-40) cc_final: 0.8565 (m-40) REVERT: A 464 MET cc_start: 0.8832 (pmt) cc_final: 0.8327 (pmt) REVERT: A 562 LEU cc_start: 0.9172 (tp) cc_final: 0.8914 (tp) REVERT: A 618 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8175 (tppt) REVERT: A 622 ASP cc_start: 0.9480 (m-30) cc_final: 0.8785 (t0) REVERT: A 626 MET cc_start: 0.9333 (mmp) cc_final: 0.8844 (mmp) REVERT: A 906 MET cc_start: 0.7491 (tmm) cc_final: 0.7290 (tmm) REVERT: A 908 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8117 (p) outliers start: 24 outliers final: 17 residues processed: 82 average time/residue: 0.2102 time to fit residues: 25.3530 Evaluate side-chains 82 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9738 Z= 0.163 Angle : 0.552 9.562 13195 Z= 0.272 Chirality : 0.042 0.235 1471 Planarity : 0.004 0.051 1707 Dihedral : 4.764 58.134 1327 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.17 % Allowed : 11.03 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.72 (0.26), residues: 1199 helix: 2.05 (0.24), residues: 502 sheet: 0.55 (0.36), residues: 216 loop : 0.59 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 33 HIS 0.002 0.000 HIS A 305 PHE 0.009 0.001 PHE A 985 TYR 0.008 0.001 TYR A 627 ARG 0.004 0.000 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8830 (p) REVERT: A 218 MET cc_start: 0.3601 (mmm) cc_final: 0.3335 (mmm) REVERT: A 235 TYR cc_start: 0.8360 (m-80) cc_final: 0.8030 (m-10) REVERT: A 285 MET cc_start: 0.8804 (pmm) cc_final: 0.8369 (pmm) REVERT: A 345 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8840 (mm-30) REVERT: A 353 ASP cc_start: 0.8436 (t0) cc_final: 0.7776 (m-30) REVERT: A 445 ASN cc_start: 0.9111 (m-40) cc_final: 0.8568 (m-40) REVERT: A 464 MET cc_start: 0.8839 (pmt) cc_final: 0.8383 (pmt) REVERT: A 562 LEU cc_start: 0.9172 (tp) cc_final: 0.8914 (tp) REVERT: A 618 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8220 (tppt) REVERT: A 622 ASP cc_start: 0.9476 (m-30) cc_final: 0.8786 (t0) REVERT: A 626 MET cc_start: 0.9323 (mmp) cc_final: 0.8853 (mmp) REVERT: A 707 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8437 (mtt180) REVERT: A 906 MET cc_start: 0.7406 (tmm) cc_final: 0.7197 (tmm) REVERT: A 908 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8029 (p) outliers start: 23 outliers final: 17 residues processed: 85 average time/residue: 0.2135 time to fit residues: 27.1464 Evaluate side-chains 81 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9738 Z= 0.184 Angle : 0.582 10.352 13195 Z= 0.285 Chirality : 0.042 0.230 1471 Planarity : 0.003 0.049 1707 Dihedral : 4.740 57.206 1327 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.07 % Allowed : 11.12 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.71 (0.26), residues: 1199 helix: 2.08 (0.24), residues: 502 sheet: 0.50 (0.37), residues: 214 loop : 0.56 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.002 0.001 HIS A 458 PHE 0.009 0.001 PHE A 985 TYR 0.012 0.001 TYR D 59 ARG 0.004 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8800 (p) REVERT: A 218 MET cc_start: 0.3594 (mmm) cc_final: 0.3296 (mmm) REVERT: A 235 TYR cc_start: 0.8387 (m-80) cc_final: 0.8041 (m-10) REVERT: A 285 MET cc_start: 0.8796 (pmm) cc_final: 0.8348 (pmm) REVERT: A 345 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8832 (mm-30) REVERT: A 353 ASP cc_start: 0.8491 (t0) cc_final: 0.7842 (m-30) REVERT: A 445 ASN cc_start: 0.9119 (m-40) cc_final: 0.8596 (m-40) REVERT: A 464 MET cc_start: 0.8831 (pmt) cc_final: 0.8344 (pmt) REVERT: A 562 LEU cc_start: 0.9131 (tp) cc_final: 0.8861 (tp) REVERT: A 618 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8235 (tppt) REVERT: A 622 ASP cc_start: 0.9480 (m-30) cc_final: 0.8790 (t0) REVERT: A 626 MET cc_start: 0.9335 (mmp) cc_final: 0.8893 (mmp) REVERT: A 906 MET cc_start: 0.7412 (tmm) cc_final: 0.7192 (tmm) REVERT: A 908 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8041 (p) outliers start: 22 outliers final: 17 residues processed: 79 average time/residue: 0.2110 time to fit residues: 24.5669 Evaluate side-chains 80 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 109 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9738 Z= 0.203 Angle : 0.613 10.834 13195 Z= 0.302 Chirality : 0.042 0.185 1471 Planarity : 0.004 0.049 1707 Dihedral : 4.755 56.846 1327 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.79 % Allowed : 11.50 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.64 (0.26), residues: 1199 helix: 2.03 (0.24), residues: 502 sheet: 0.43 (0.37), residues: 214 loop : 0.54 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.002 0.001 HIS A 458 PHE 0.027 0.001 PHE D 4 TYR 0.009 0.001 TYR A 627 ARG 0.003 0.000 ARG D 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8810 (p) REVERT: A 218 MET cc_start: 0.3599 (mmm) cc_final: 0.3293 (mmm) REVERT: A 235 TYR cc_start: 0.8418 (m-80) cc_final: 0.8062 (m-10) REVERT: A 285 MET cc_start: 0.8809 (pmm) cc_final: 0.8335 (pmm) REVERT: A 345 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8840 (mm-30) REVERT: A 353 ASP cc_start: 0.8512 (t0) cc_final: 0.8290 (t0) REVERT: A 445 ASN cc_start: 0.9126 (m-40) cc_final: 0.8601 (m-40) REVERT: A 464 MET cc_start: 0.8824 (pmt) cc_final: 0.8341 (pmt) REVERT: A 562 LEU cc_start: 0.9135 (tp) cc_final: 0.8882 (tp) REVERT: A 618 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8184 (tppt) REVERT: A 622 ASP cc_start: 0.9484 (m-30) cc_final: 0.8794 (t0) REVERT: A 626 MET cc_start: 0.9339 (mmp) cc_final: 0.8899 (mmp) REVERT: A 906 MET cc_start: 0.7435 (tmm) cc_final: 0.7227 (tmm) REVERT: A 908 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8072 (p) outliers start: 19 outliers final: 16 residues processed: 80 average time/residue: 0.2126 time to fit residues: 25.2490 Evaluate side-chains 78 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 94 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.0030 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.050594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.039338 restraints weight = 60111.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.040603 restraints weight = 35418.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041471 restraints weight = 24342.546| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9738 Z= 0.150 Angle : 0.613 10.456 13195 Z= 0.296 Chirality : 0.043 0.369 1471 Planarity : 0.003 0.049 1707 Dihedral : 4.429 53.155 1326 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.41 % Allowed : 11.88 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.58 (0.26), residues: 1199 helix: 1.94 (0.24), residues: 502 sheet: 0.51 (0.37), residues: 212 loop : 0.49 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 33 HIS 0.001 0.000 HIS C 125 PHE 0.023 0.001 PHE D 4 TYR 0.007 0.001 TYR C 127 ARG 0.003 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1855.29 seconds wall clock time: 33 minutes 50.44 seconds (2030.44 seconds total)