Starting phenix.real_space_refine on Sat Aug 3 22:42:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5m_44217/08_2024/9b5m_44217.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5m_44217/08_2024/9b5m_44217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5m_44217/08_2024/9b5m_44217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5m_44217/08_2024/9b5m_44217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5m_44217/08_2024/9b5m_44217.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5m_44217/08_2024/9b5m_44217.cif" } resolution = 2.79 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= 0.062 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 41 5.16 5 C 5703 2.51 5 N 1470 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "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: 8935 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} 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: 6.11, per 1000 atoms: 0.68 Number of scatterers: 8935 At special positions: 0 Unit cell: (84.056, 100.016, 119.168, 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 41 16.00 P 3 15.00 Mg 2 11.99 O 1716 8.00 N 1470 7.00 C 5703 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=2.91 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: 3.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 48.5% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.780A 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: 3.708A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.918A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.392A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.518A 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: 3.742A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.562A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.290A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.619A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.593A 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 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.335A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.525A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.654A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.542A 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 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.847A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.824A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.509A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.565A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' 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 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.669A 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 removed outlier: 3.538A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.554A 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: 4.008A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.883A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) 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: 3.633A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.565A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' 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 sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.880A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.271A 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: 4.166A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.183A 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: 4.166A 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: 6.452A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.165A 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 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.394A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.516A 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 922 removed outlier: 6.394A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.383A 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 26 removed outlier: 3.656A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1209 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: 3.36 Time building geometry restraints manager: 3.85 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: 1512 1.27 - 1.40: 2173 1.40 - 1.54: 5272 1.54 - 1.67: 121 1.67 - 1.81: 62 Bond restraints: 9140 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.29e+01 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 9.24e-01 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 8.68e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.404 0.012 1.30e-02 5.92e+03 8.24e-01 bond pdb=" CA ASP A 335 " pdb=" C ASP A 335 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.54e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 100.00 - 115.86: 5967 115.86 - 131.73: 6411 131.73 - 147.60: 11 147.60 - 163.46: 0 163.46 - 179.33: 1 Bond angle restraints: 12390 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 121.70 128.54 -6.84 1.80e+00 3.09e-01 1.44e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.17 3.36 1.18e+00 7.24e-01 8.19e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.70 4.49 1.76e+00 3.23e-01 6.52e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.60 6.23 2.67e+00 1.40e-01 5.44e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.55 6.03 2.79e+00 1.28e-01 4.66e+00 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5339 17.78 - 35.57: 166 35.57 - 53.35: 36 53.35 - 71.13: 8 71.13 - 88.92: 3 Dihedral angle restraints: 5552 sinusoidal: 2262 harmonic: 3290 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 -141.25 55.25 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LEU A 870 " pdb=" CB LEU A 870 " pdb=" CG LEU A 870 " pdb=" CD1 LEU A 870 " ideal model delta sinusoidal sigma weight residual 60.00 119.39 -59.39 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1210 0.056 - 0.112: 131 0.112 - 0.167: 30 0.167 - 0.223: 0 0.223 - 0.279: 3 Chirality restraints: 1374 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 -2.96 0.28 2.00e-01 2.50e+01 1.95e+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 -2.90 0.27 2.00e-01 2.50e+01 1.80e+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 -2.72 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1371 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO C 95 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO C 18 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 90 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.20e-01 pdb=" N PRO A 91 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.013 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 64 2.61 - 3.18: 7688 3.18 - 3.75: 13075 3.75 - 4.33: 19674 4.33 - 4.90: 32681 Nonbonded interactions: 73182 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.034 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.035 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.085 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.108 2.170 nonbonded pdb=" OE1 GLU A 518 " pdb=" NH1 ARG A 986 " model vdw 2.253 3.120 ... (remaining 73177 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: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.350 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 0.072 9140 Z= 0.166 Angle : 0.446 6.841 12390 Z= 0.225 Chirality : 0.042 0.279 1374 Planarity : 0.003 0.031 1604 Dihedral : 9.700 88.918 3425 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.91 % Allowed : 2.22 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.13 (0.26), residues: 1126 helix: 1.67 (0.25), residues: 486 sheet: 0.13 (0.38), residues: 182 loop : 0.12 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 608 HIS 0.001 0.000 HIS C 75 PHE 0.009 0.001 PHE A 842 TYR 0.007 0.001 TYR A 736 ARG 0.002 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8076 (pt0) cc_final: 0.7809 (pp20) REVERT: A 182 THR cc_start: 0.8035 (t) cc_final: 0.7766 (m) REVERT: A 184 MET cc_start: 0.7588 (mtp) cc_final: 0.7341 (mtt) REVERT: A 196 MET cc_start: 0.7689 (mmp) cc_final: 0.7015 (mmp) REVERT: A 273 LYS cc_start: 0.7224 (mttt) cc_final: 0.6854 (mtmp) REVERT: A 274 ASP cc_start: 0.7601 (t70) cc_final: 0.6922 (p0) REVERT: A 341 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6947 (mmpt) REVERT: A 423 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6371 (tp30) REVERT: A 442 MET cc_start: 0.7959 (tpp) cc_final: 0.7320 (mmm) REVERT: A 596 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7388 (tttt) REVERT: A 601 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7290 (mtp180) REVERT: A 611 ASP cc_start: 0.6783 (m-30) cc_final: 0.6470 (m-30) REVERT: A 668 MET cc_start: 0.7483 (mmm) cc_final: 0.7221 (mmm) REVERT: A 754 TYR cc_start: 0.7024 (t80) cc_final: 0.6594 (t80) REVERT: A 755 ASN cc_start: 0.8345 (m-40) cc_final: 0.7659 (p0) REVERT: A 878 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7766 (mmtm) REVERT: A 879 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7347 (mttp) REVERT: A 935 GLN cc_start: 0.7513 (tp40) cc_final: 0.6921 (tt0) REVERT: A 937 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: A 979 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7358 (mmmt) REVERT: A 987 LYS cc_start: 0.8506 (mtpt) cc_final: 0.7992 (mttm) REVERT: C 59 ASP cc_start: 0.8182 (m-30) cc_final: 0.7858 (t0) REVERT: C 72 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7737 (mtp85) outliers start: 9 outliers final: 3 residues processed: 133 average time/residue: 1.5011 time to fit residues: 211.5262 Evaluate side-chains 105 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 101 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: 0.7211 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9140 Z= 0.297 Angle : 0.519 7.493 12390 Z= 0.270 Chirality : 0.044 0.146 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.277 66.925 1254 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.61 % Allowed : 6.85 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.18 (0.25), residues: 1126 helix: 1.63 (0.25), residues: 484 sheet: 0.59 (0.38), residues: 174 loop : 0.06 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 202 PHE 0.012 0.002 PHE A 321 TYR 0.011 0.002 TYR C 74 ARG 0.008 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.021 Fit side-chains REVERT: A 114 GLU cc_start: 0.8098 (pt0) cc_final: 0.7820 (pp20) REVERT: A 182 THR cc_start: 0.8228 (t) cc_final: 0.7927 (m) REVERT: A 184 MET cc_start: 0.7654 (mtp) cc_final: 0.7366 (mtt) REVERT: A 196 MET cc_start: 0.7843 (mmp) cc_final: 0.7326 (mmp) REVERT: A 273 LYS cc_start: 0.7274 (mttt) cc_final: 0.6908 (mtmp) REVERT: A 274 ASP cc_start: 0.7663 (t70) cc_final: 0.6924 (p0) REVERT: A 423 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6436 (tp30) REVERT: A 596 LYS cc_start: 0.7827 (tmtt) cc_final: 0.7290 (tttt) REVERT: A 601 ARG cc_start: 0.6956 (mtm-85) cc_final: 0.6641 (mtp85) REVERT: A 611 ASP cc_start: 0.6941 (m-30) cc_final: 0.6533 (m-30) REVERT: A 652 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6718 (ttt-90) REVERT: A 699 GLN cc_start: 0.8081 (mp10) cc_final: 0.7444 (mp10) REVERT: A 755 ASN cc_start: 0.8158 (m-40) cc_final: 0.7357 (p0) REVERT: A 762 LYS cc_start: 0.8265 (pttm) cc_final: 0.7851 (mmtt) REVERT: A 879 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7414 (mttp) REVERT: A 935 GLN cc_start: 0.7546 (tp40) cc_final: 0.6952 (tt0) REVERT: A 937 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 979 LYS cc_start: 0.7671 (mmtp) cc_final: 0.7356 (mmmt) REVERT: A 987 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8000 (mttp) REVERT: A 1011 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7288 (tttp) REVERT: C 59 ASP cc_start: 0.8169 (m-30) cc_final: 0.7959 (t0) REVERT: C 72 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7683 (mtp85) outliers start: 16 outliers final: 5 residues processed: 113 average time/residue: 1.5952 time to fit residues: 190.1217 Evaluate side-chains 108 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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: 0.7203 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9140 Z= 0.232 Angle : 0.507 12.232 12390 Z= 0.262 Chirality : 0.042 0.181 1374 Planarity : 0.004 0.044 1604 Dihedral : 6.067 63.259 1253 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.31 % Allowed : 8.87 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.17 (0.25), residues: 1126 helix: 1.61 (0.24), residues: 486 sheet: 0.58 (0.38), residues: 174 loop : 0.07 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.002 0.001 HIS A 202 PHE 0.010 0.001 PHE A 321 TYR 0.012 0.001 TYR C 74 ARG 0.007 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.079 Fit side-chains REVERT: A 114 GLU cc_start: 0.8094 (pt0) cc_final: 0.7824 (pp20) REVERT: A 182 THR cc_start: 0.8323 (t) cc_final: 0.8070 (m) REVERT: A 184 MET cc_start: 0.7524 (mtp) cc_final: 0.7036 (mtt) REVERT: A 196 MET cc_start: 0.7846 (mmp) cc_final: 0.7607 (mmm) REVERT: A 273 LYS cc_start: 0.7414 (mttt) cc_final: 0.7068 (mtmp) REVERT: A 274 ASP cc_start: 0.7656 (t70) cc_final: 0.6915 (p0) REVERT: A 341 LYS cc_start: 0.7246 (mmmt) cc_final: 0.6963 (mmpt) REVERT: A 423 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6347 (tp30) REVERT: A 596 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7287 (tttt) REVERT: A 601 ARG cc_start: 0.6991 (mtm-85) cc_final: 0.6683 (mtp85) REVERT: A 611 ASP cc_start: 0.6921 (m-30) cc_final: 0.6499 (m-30) REVERT: A 699 GLN cc_start: 0.8122 (mp10) cc_final: 0.7362 (mp10) REVERT: A 755 ASN cc_start: 0.8214 (m-40) cc_final: 0.7471 (p0) REVERT: A 878 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7488 (mmtm) REVERT: A 879 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7406 (mttp) REVERT: A 935 GLN cc_start: 0.7554 (tp40) cc_final: 0.6960 (tt0) REVERT: A 937 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: A 979 LYS cc_start: 0.7648 (mmtp) cc_final: 0.7314 (mmmt) REVERT: A 987 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7970 (mttm) REVERT: A 1011 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7247 (tttp) REVERT: C 59 ASP cc_start: 0.8131 (m-30) cc_final: 0.7861 (t0) REVERT: C 72 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7752 (mtp85) outliers start: 13 outliers final: 7 residues processed: 112 average time/residue: 1.4778 time to fit residues: 175.0883 Evaluate side-chains 110 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.7204 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9140 Z= 0.232 Angle : 0.497 10.984 12390 Z= 0.257 Chirality : 0.042 0.158 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.018 60.930 1253 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.51 % Allowed : 9.07 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.16 (0.25), residues: 1126 helix: 1.60 (0.24), residues: 485 sheet: 0.55 (0.38), residues: 174 loop : 0.09 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE A 321 TYR 0.013 0.001 TYR C 74 ARG 0.008 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.971 Fit side-chains REVERT: A 114 GLU cc_start: 0.8100 (pt0) cc_final: 0.7828 (pp20) REVERT: A 182 THR cc_start: 0.8361 (t) cc_final: 0.8118 (m) REVERT: A 184 MET cc_start: 0.7446 (mtp) cc_final: 0.6937 (mtt) REVERT: A 196 MET cc_start: 0.7839 (mmp) cc_final: 0.7609 (mmm) REVERT: A 273 LYS cc_start: 0.7413 (mttt) cc_final: 0.7195 (mttp) REVERT: A 274 ASP cc_start: 0.7658 (t70) cc_final: 0.6910 (p0) REVERT: A 333 GLN cc_start: 0.7859 (mp10) cc_final: 0.7575 (mp10) REVERT: A 341 LYS cc_start: 0.7237 (mmmt) cc_final: 0.6956 (mmpt) REVERT: A 423 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6492 (tp30) REVERT: A 465 ASP cc_start: 0.8336 (t0) cc_final: 0.8014 (t0) REVERT: A 596 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7199 (tttt) REVERT: A 601 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6667 (mtp85) REVERT: A 611 ASP cc_start: 0.6936 (m-30) cc_final: 0.6529 (m-30) REVERT: A 699 GLN cc_start: 0.8166 (mp10) cc_final: 0.7826 (mp10) REVERT: A 755 ASN cc_start: 0.8221 (m-40) cc_final: 0.7518 (p0) REVERT: A 869 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: A 878 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7515 (mmtm) REVERT: A 879 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7390 (mttp) REVERT: A 935 GLN cc_start: 0.7582 (tp40) cc_final: 0.6982 (tt0) REVERT: A 937 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 979 LYS cc_start: 0.7677 (mmtp) cc_final: 0.7322 (mmmt) REVERT: A 987 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7967 (mttm) REVERT: A 1011 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7249 (tttp) REVERT: C 32 HIS cc_start: 0.7986 (t-170) cc_final: 0.7773 (t70) REVERT: C 59 ASP cc_start: 0.8126 (m-30) cc_final: 0.7856 (t0) REVERT: C 72 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7767 (mtp85) outliers start: 15 outliers final: 7 residues processed: 110 average time/residue: 1.5490 time to fit residues: 180.1807 Evaluate side-chains 108 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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: 0.7210 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9140 Z= 0.263 Angle : 0.501 10.539 12390 Z= 0.259 Chirality : 0.043 0.154 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.019 60.410 1253 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.02 % Allowed : 9.58 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.11 (0.25), residues: 1126 helix: 1.57 (0.24), residues: 485 sheet: 0.52 (0.37), residues: 180 loop : 0.04 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.010 0.001 PHE A 321 TYR 0.014 0.001 TYR C 74 ARG 0.008 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.034 Fit side-chains REVERT: A 32 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7309 (mmm) REVERT: A 114 GLU cc_start: 0.8105 (pt0) cc_final: 0.7828 (pp20) REVERT: A 182 THR cc_start: 0.8379 (t) cc_final: 0.8137 (m) REVERT: A 184 MET cc_start: 0.7723 (mtp) cc_final: 0.7156 (mtt) REVERT: A 196 MET cc_start: 0.7842 (mmp) cc_final: 0.7620 (mmm) REVERT: A 273 LYS cc_start: 0.7409 (mttt) cc_final: 0.7197 (mttp) REVERT: A 274 ASP cc_start: 0.7669 (t70) cc_final: 0.6890 (p0) REVERT: A 306 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: A 333 GLN cc_start: 0.7710 (mp10) cc_final: 0.7461 (mp10) REVERT: A 423 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6497 (tp30) REVERT: A 465 ASP cc_start: 0.8366 (t0) cc_final: 0.8043 (t0) REVERT: A 596 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7255 (tttt) REVERT: A 601 ARG cc_start: 0.6996 (mtm-85) cc_final: 0.6656 (mtp85) REVERT: A 611 ASP cc_start: 0.6934 (m-30) cc_final: 0.6534 (m-30) REVERT: A 699 GLN cc_start: 0.8169 (mp10) cc_final: 0.7806 (mp10) REVERT: A 755 ASN cc_start: 0.8207 (m-40) cc_final: 0.7511 (p0) REVERT: A 869 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 878 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7593 (mmtm) REVERT: A 879 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7392 (mttp) REVERT: A 935 GLN cc_start: 0.7589 (tp40) cc_final: 0.6984 (tt0) REVERT: A 937 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: A 979 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7321 (mmmt) REVERT: A 987 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7973 (mttm) REVERT: A 1011 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7279 (tttp) REVERT: C 32 HIS cc_start: 0.7988 (t-170) cc_final: 0.7759 (t70) REVERT: C 59 ASP cc_start: 0.8122 (m-30) cc_final: 0.7849 (t0) REVERT: C 72 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7771 (mtp85) outliers start: 20 outliers final: 8 residues processed: 114 average time/residue: 1.4349 time to fit residues: 173.5658 Evaluate side-chains 112 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.2980 chunk 21 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 104 optimal weight: 0.5980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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: 0.7189 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9140 Z= 0.159 Angle : 0.472 9.859 12390 Z= 0.243 Chirality : 0.041 0.163 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.861 57.750 1253 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.61 % Allowed : 10.18 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.29 (0.26), residues: 1126 helix: 1.74 (0.24), residues: 485 sheet: 0.61 (0.37), residues: 181 loop : 0.10 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.008 0.001 PHE A 321 TYR 0.012 0.001 TYR C 74 ARG 0.007 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.967 Fit side-chains REVERT: A 114 GLU cc_start: 0.8078 (pt0) cc_final: 0.7834 (pp20) REVERT: A 182 THR cc_start: 0.8397 (t) cc_final: 0.8167 (m) REVERT: A 184 MET cc_start: 0.7474 (mtp) cc_final: 0.7030 (mtt) REVERT: A 196 MET cc_start: 0.7862 (mmp) cc_final: 0.7258 (mmp) REVERT: A 229 VAL cc_start: 0.6942 (t) cc_final: 0.6587 (p) REVERT: A 273 LYS cc_start: 0.7397 (mttt) cc_final: 0.7187 (mttp) REVERT: A 274 ASP cc_start: 0.7662 (t70) cc_final: 0.6881 (p0) REVERT: A 333 GLN cc_start: 0.7709 (mp10) cc_final: 0.7453 (mp10) REVERT: A 423 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6320 (tp30) REVERT: A 465 ASP cc_start: 0.8384 (t0) cc_final: 0.8048 (t0) REVERT: A 596 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7254 (tttt) REVERT: A 601 ARG cc_start: 0.6913 (mtm-85) cc_final: 0.6679 (mtp180) REVERT: A 611 ASP cc_start: 0.6903 (m-30) cc_final: 0.6488 (m-30) REVERT: A 699 GLN cc_start: 0.8178 (mp10) cc_final: 0.7798 (mp10) REVERT: A 755 ASN cc_start: 0.8205 (m-40) cc_final: 0.7510 (p0) REVERT: A 879 LYS cc_start: 0.7886 (mmmm) cc_final: 0.7331 (mttp) REVERT: A 935 GLN cc_start: 0.7581 (tp40) cc_final: 0.6967 (tt0) REVERT: A 937 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 979 LYS cc_start: 0.7694 (mmtp) cc_final: 0.7312 (mmmt) REVERT: A 987 LYS cc_start: 0.8448 (mtpt) cc_final: 0.7973 (mttm) REVERT: A 1011 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7223 (tttp) REVERT: C 32 HIS cc_start: 0.7998 (t-170) cc_final: 0.7771 (t70) REVERT: C 59 ASP cc_start: 0.8090 (m-30) cc_final: 0.7806 (t0) REVERT: C 72 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7759 (mtp85) outliers start: 16 outliers final: 6 residues processed: 109 average time/residue: 1.5101 time to fit residues: 173.7758 Evaluate side-chains 105 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 66 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7200 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9140 Z= 0.228 Angle : 0.491 9.861 12390 Z= 0.253 Chirality : 0.042 0.163 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.935 57.862 1253 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.41 % Allowed : 10.69 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.25 (0.25), residues: 1126 helix: 1.69 (0.24), residues: 485 sheet: 0.62 (0.37), residues: 180 loop : 0.10 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 PHE 0.010 0.001 PHE A 321 TYR 0.013 0.001 TYR C 74 ARG 0.007 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.033 Fit side-chains REVERT: A 32 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7332 (mmm) REVERT: A 114 GLU cc_start: 0.8092 (pt0) cc_final: 0.7836 (pp20) REVERT: A 182 THR cc_start: 0.8402 (t) cc_final: 0.8178 (m) REVERT: A 184 MET cc_start: 0.7632 (mtp) cc_final: 0.7183 (mtt) REVERT: A 196 MET cc_start: 0.7871 (mmp) cc_final: 0.7268 (mmp) REVERT: A 273 LYS cc_start: 0.7393 (mttt) cc_final: 0.7173 (mttp) REVERT: A 274 ASP cc_start: 0.7685 (t70) cc_final: 0.6885 (p0) REVERT: A 333 GLN cc_start: 0.7771 (mp10) cc_final: 0.7550 (mp10) REVERT: A 423 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6507 (tp30) REVERT: A 465 ASP cc_start: 0.8372 (t0) cc_final: 0.8037 (t0) REVERT: A 596 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7310 (tttt) REVERT: A 601 ARG cc_start: 0.6958 (mtm-85) cc_final: 0.6718 (mtp180) REVERT: A 611 ASP cc_start: 0.6907 (m-30) cc_final: 0.6492 (m-30) REVERT: A 699 GLN cc_start: 0.8126 (mp10) cc_final: 0.7756 (mp10) REVERT: A 755 ASN cc_start: 0.8200 (m-40) cc_final: 0.7505 (p0) REVERT: A 878 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7576 (mmtm) REVERT: A 879 LYS cc_start: 0.7906 (mmmm) cc_final: 0.7381 (mttp) REVERT: A 935 GLN cc_start: 0.7585 (tp40) cc_final: 0.6971 (tt0) REVERT: A 937 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 969 LYS cc_start: 0.7074 (mtmt) cc_final: 0.6796 (mtpp) REVERT: A 979 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7297 (mmmt) REVERT: A 987 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7972 (mttm) REVERT: A 1011 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7236 (tttp) REVERT: C 32 HIS cc_start: 0.7942 (t-170) cc_final: 0.7671 (t70) REVERT: C 59 ASP cc_start: 0.8121 (m-30) cc_final: 0.7844 (t0) REVERT: C 72 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7759 (mtp85) outliers start: 14 outliers final: 7 residues processed: 109 average time/residue: 1.6131 time to fit residues: 185.6632 Evaluate side-chains 108 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7213 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9140 Z= 0.296 Angle : 0.519 9.992 12390 Z= 0.267 Chirality : 0.043 0.161 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.987 58.076 1253 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.41 % Allowed : 10.99 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.14 (0.25), residues: 1126 helix: 1.59 (0.24), residues: 485 sheet: 0.56 (0.38), residues: 175 loop : 0.04 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS C 125 PHE 0.011 0.001 PHE A 321 TYR 0.014 0.001 TYR C 74 ARG 0.008 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.029 Fit side-chains REVERT: A 32 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7332 (mmm) REVERT: A 114 GLU cc_start: 0.8111 (pt0) cc_final: 0.7797 (pp20) REVERT: A 182 THR cc_start: 0.8429 (t) cc_final: 0.8194 (m) REVERT: A 184 MET cc_start: 0.7635 (mtp) cc_final: 0.7193 (mtt) REVERT: A 196 MET cc_start: 0.7880 (mmp) cc_final: 0.7279 (mmp) REVERT: A 273 LYS cc_start: 0.7396 (mttt) cc_final: 0.7172 (mttp) REVERT: A 274 ASP cc_start: 0.7692 (t70) cc_final: 0.6882 (p0) REVERT: A 333 GLN cc_start: 0.7775 (mp10) cc_final: 0.7572 (mp10) REVERT: A 423 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6504 (tp30) REVERT: A 465 ASP cc_start: 0.8332 (t0) cc_final: 0.8019 (t0) REVERT: A 596 LYS cc_start: 0.7790 (tmtt) cc_final: 0.7371 (tttt) REVERT: A 601 ARG cc_start: 0.6920 (mtm-85) cc_final: 0.6719 (mtp180) REVERT: A 611 ASP cc_start: 0.6935 (m-30) cc_final: 0.6527 (m-30) REVERT: A 699 GLN cc_start: 0.8131 (mp10) cc_final: 0.7756 (mp10) REVERT: A 755 ASN cc_start: 0.8196 (m-40) cc_final: 0.7498 (p0) REVERT: A 878 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7588 (mmtm) REVERT: A 879 LYS cc_start: 0.7911 (mmmm) cc_final: 0.7386 (mttp) REVERT: A 935 GLN cc_start: 0.7595 (tp40) cc_final: 0.6982 (tt0) REVERT: A 937 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 969 LYS cc_start: 0.7079 (mtmt) cc_final: 0.6802 (mtpp) REVERT: A 979 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7306 (mmmt) REVERT: A 987 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7960 (mttm) REVERT: A 1011 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7271 (tttp) REVERT: C 32 HIS cc_start: 0.7968 (t-170) cc_final: 0.7700 (t70) REVERT: C 59 ASP cc_start: 0.8131 (m-30) cc_final: 0.7850 (t0) REVERT: C 72 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7766 (mtp85) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 1.5504 time to fit residues: 175.3758 Evaluate side-chains 111 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7207 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9140 Z= 0.245 Angle : 0.503 9.813 12390 Z= 0.260 Chirality : 0.042 0.153 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.959 58.106 1253 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.31 % Allowed : 11.49 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.15 (0.25), residues: 1126 helix: 1.61 (0.24), residues: 485 sheet: 0.56 (0.38), residues: 175 loop : 0.05 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.010 0.001 PHE A 321 TYR 0.013 0.001 TYR C 74 ARG 0.008 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.022 Fit side-chains REVERT: A 32 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7339 (mmm) REVERT: A 114 GLU cc_start: 0.8106 (pt0) cc_final: 0.7795 (pp20) REVERT: A 182 THR cc_start: 0.8427 (t) cc_final: 0.8191 (m) REVERT: A 184 MET cc_start: 0.7632 (mtp) cc_final: 0.7223 (mtt) REVERT: A 196 MET cc_start: 0.7879 (mmp) cc_final: 0.7277 (mmp) REVERT: A 273 LYS cc_start: 0.7390 (mttt) cc_final: 0.7170 (mttp) REVERT: A 274 ASP cc_start: 0.7691 (t70) cc_final: 0.6881 (p0) REVERT: A 333 GLN cc_start: 0.7762 (mp10) cc_final: 0.7551 (mp10) REVERT: A 423 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6502 (tp30) REVERT: A 465 ASP cc_start: 0.8389 (t0) cc_final: 0.8019 (t0) REVERT: A 596 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7368 (tttt) REVERT: A 601 ARG cc_start: 0.6896 (mtm-85) cc_final: 0.6691 (mtp180) REVERT: A 611 ASP cc_start: 0.6867 (m-30) cc_final: 0.6458 (m-30) REVERT: A 699 GLN cc_start: 0.8133 (mp10) cc_final: 0.7756 (mp10) REVERT: A 755 ASN cc_start: 0.8169 (m-40) cc_final: 0.7556 (p0) REVERT: A 879 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7428 (mttp) REVERT: A 935 GLN cc_start: 0.7594 (tp40) cc_final: 0.6980 (tt0) REVERT: A 937 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 969 LYS cc_start: 0.7070 (mtmt) cc_final: 0.6800 (mtpp) REVERT: A 979 LYS cc_start: 0.7704 (mmtp) cc_final: 0.7306 (mmmt) REVERT: A 987 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7966 (mttm) REVERT: A 1011 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7277 (tttp) REVERT: C 32 HIS cc_start: 0.7952 (t-170) cc_final: 0.7683 (t70) REVERT: C 59 ASP cc_start: 0.8124 (m-30) cc_final: 0.7844 (t0) REVERT: C 72 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7762 (mtp85) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 1.5330 time to fit residues: 173.3771 Evaluate side-chains 107 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0030 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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: 0.7199 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9140 Z= 0.207 Angle : 0.495 9.582 12390 Z= 0.254 Chirality : 0.042 0.159 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.895 58.203 1253 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.01 % Allowed : 11.59 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.20 (0.25), residues: 1126 helix: 1.66 (0.24), residues: 485 sheet: 0.58 (0.38), residues: 175 loop : 0.06 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.009 0.001 PHE A 321 TYR 0.012 0.001 TYR C 74 ARG 0.008 0.000 ARG C 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.018 Fit side-chains REVERT: A 32 MET cc_start: 0.7664 (mtp) cc_final: 0.7337 (mmm) REVERT: A 114 GLU cc_start: 0.8101 (pt0) cc_final: 0.7795 (pp20) REVERT: A 182 THR cc_start: 0.8436 (t) cc_final: 0.8191 (m) REVERT: A 184 MET cc_start: 0.7632 (mtp) cc_final: 0.7219 (mtt) REVERT: A 196 MET cc_start: 0.7875 (mmp) cc_final: 0.7277 (mmp) REVERT: A 273 LYS cc_start: 0.7362 (mttt) cc_final: 0.7143 (mttp) REVERT: A 274 ASP cc_start: 0.7689 (t70) cc_final: 0.6880 (p0) REVERT: A 333 GLN cc_start: 0.7762 (mp10) cc_final: 0.7549 (mp10) REVERT: A 423 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6496 (tp30) REVERT: A 465 ASP cc_start: 0.8391 (t0) cc_final: 0.8027 (t0) REVERT: A 596 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7384 (tttt) REVERT: A 611 ASP cc_start: 0.6904 (m-30) cc_final: 0.6489 (m-30) REVERT: A 699 GLN cc_start: 0.8167 (mp10) cc_final: 0.7806 (mp10) REVERT: A 755 ASN cc_start: 0.8165 (m-40) cc_final: 0.7557 (p0) REVERT: A 879 LYS cc_start: 0.7928 (mmmm) cc_final: 0.7384 (mttp) REVERT: A 935 GLN cc_start: 0.7590 (tp40) cc_final: 0.6974 (tt0) REVERT: A 937 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 969 LYS cc_start: 0.7067 (mtmt) cc_final: 0.6795 (mtpp) REVERT: A 979 LYS cc_start: 0.7701 (mmtp) cc_final: 0.7303 (mmmt) REVERT: A 987 LYS cc_start: 0.8426 (mtpt) cc_final: 0.7967 (mttm) REVERT: A 1011 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7270 (tttp) REVERT: C 32 HIS cc_start: 0.7910 (t-170) cc_final: 0.7638 (t70) REVERT: C 59 ASP cc_start: 0.8089 (m-30) cc_final: 0.7826 (t0) REVERT: C 72 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7761 (mtp85) outliers start: 10 outliers final: 8 residues processed: 105 average time/residue: 1.5494 time to fit residues: 171.9458 Evaluate side-chains 106 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.130430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.090124 restraints weight = 11177.642| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.50 r_work: 0.2896 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9140 Z= 0.262 Angle : 0.504 9.711 12390 Z= 0.260 Chirality : 0.043 0.152 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.921 58.122 1253 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.11 % Allowed : 11.39 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.14 (0.25), residues: 1126 helix: 1.59 (0.24), residues: 485 sheet: 0.54 (0.38), residues: 175 loop : 0.06 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.011 0.001 PHE A 321 TYR 0.013 0.001 TYR C 74 ARG 0.004 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3592.16 seconds wall clock time: 63 minutes 29.33 seconds (3809.33 seconds total)