Starting phenix.real_space_refine on Thu Jan 16 14:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5h_44212/01_2025/9b5h_44212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5h_44212/01_2025/9b5h_44212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5h_44212/01_2025/9b5h_44212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5h_44212/01_2025/9b5h_44212.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5h_44212/01_2025/9b5h_44212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5h_44212/01_2025/9b5h_44212.cif" } resolution = 2.69 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= 0.071 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 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 7 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: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: 6.71, per 1000 atoms: 0.70 Number of scatterers: 9536 At special positions: 0 Unit cell: (86.184, 98.952, 120.232, 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 1836 8.00 N 1575 7.00 C 6078 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 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: 52 helices and 10 sheets defined 47.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.717A 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: 3.692A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.021A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.293A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.520A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.643A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 4.146A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.319A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.599A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.603A 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: 4.378A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.536A 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: 3.523A 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: 3.934A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.850A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.601A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.531A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.910A 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 640 removed outlier: 3.992A 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: 3.595A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.979A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.511A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.645A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.767A 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 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 86 through 90 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: 6.791A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.290A 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: 4.158A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.299A 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: 4.158A 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: 6.553A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.216A 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 923 removed outlier: 6.419A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.736A 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: 6.630A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.368A 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: 6.419A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.889A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 6.241A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1269 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: 3.62 Time building geometry restraints manager: 2.67 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: 1619 1.27 - 1.40: 2291 1.40 - 1.54: 5639 1.54 - 1.67: 132 1.67 - 1.81: 64 Bond restraints: 9745 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O POP A1103 " pdb=" P1 POP A1103 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 1.661 1.611 0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 9740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 13147 3.26 - 6.52: 49 6.52 - 9.78: 3 9.78 - 13.03: 0 13.03 - 16.29: 1 Bond angle restraints: 13200 Sorted by residual: angle pdb=" P1 POP A1103 " pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 139.66 123.37 16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.78 -7.08 1.80e+00 3.09e-01 1.55e+01 angle pdb=" O POP A1103 " pdb=" P1 POP A1103 " pdb=" O2 POP A1103 " ideal model delta sigma weight residual 102.11 110.62 -8.51 3.00e+00 1.11e-01 8.05e+00 angle pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.78 4.12 1.50e+00 4.44e-01 7.53e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.60 112.51 7.09 3.00e+00 1.11e-01 5.59e+00 ... (remaining 13195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5640 17.22 - 34.44: 218 34.44 - 51.65: 44 51.65 - 68.87: 5 68.87 - 86.09: 4 Dihedral angle restraints: 5911 sinusoidal: 2405 harmonic: 3506 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 -142.16 56.16 1 1.00e+01 1.00e-02 4.25e+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 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR A 277 " pdb=" C TYR A 277 " pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 915 0.030 - 0.060: 389 0.060 - 0.090: 79 0.090 - 0.120: 73 0.120 - 0.150: 15 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CA ILE B 13 " pdb=" N ILE B 13 " pdb=" C ILE B 13 " pdb=" CB ILE B 13 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA VAL A 852 " pdb=" N VAL A 852 " pdb=" C VAL A 852 " pdb=" CB VAL A 852 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE A 188 " pdb=" N ILE A 188 " pdb=" C ILE A 188 " pdb=" CB ILE A 188 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 95 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO C 121 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 76 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.017 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 40 2.56 - 3.14: 7429 3.14 - 3.73: 14057 3.73 - 4.31: 21271 4.31 - 4.90: 35822 Nonbonded interactions: 78619 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O6 POP A1103 " model vdw 1.969 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2 POP A1103 " model vdw 2.035 2.170 nonbonded pdb="MG MG A1102 " pdb=" O4 POP A1103 " model vdw 2.049 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.064 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.230 3.040 ... (remaining 78614 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 0.073 9745 Z= 0.177 Angle : 0.500 16.293 13200 Z= 0.242 Chirality : 0.040 0.150 1471 Planarity : 0.004 0.042 1709 Dihedral : 10.008 86.090 3644 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.85 % Allowed : 3.58 % Favored : 95.57 % 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: 1.11 (0.24), residues: 1200 helix: 1.42 (0.24), residues: 492 sheet: 0.81 (0.37), residues: 183 loop : 0.16 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.003 0.001 HIS A 721 PHE 0.010 0.001 PHE A 360 TYR 0.008 0.001 TYR C 74 ARG 0.003 0.000 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7214 (mmp80) cc_final: 0.6891 (mmp80) REVERT: A 196 MET cc_start: 0.8666 (mmp) cc_final: 0.8310 (mmp) REVERT: A 216 LYS cc_start: 0.6970 (mtmm) cc_final: 0.6563 (mttm) REVERT: A 250 TYR cc_start: 0.7423 (m-80) cc_final: 0.6826 (m-80) REVERT: A 262 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8461 (tmtp) REVERT: A 274 ASP cc_start: 0.7724 (t0) cc_final: 0.7201 (p0) REVERT: A 333 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8378 (mp10) REVERT: A 406 ARG cc_start: 0.7869 (mtm180) cc_final: 0.6723 (mtp85) REVERT: A 516 GLU cc_start: 0.8211 (mp0) cc_final: 0.7967 (pm20) REVERT: A 540 GLU cc_start: 0.7291 (tt0) cc_final: 0.7039 (mp0) REVERT: A 583 GLN cc_start: 0.7969 (mt0) cc_final: 0.7243 (mm110) REVERT: A 611 ASP cc_start: 0.7460 (m-30) cc_final: 0.7203 (m-30) REVERT: A 626 MET cc_start: 0.7243 (ttt) cc_final: 0.6844 (mpt) REVERT: A 668 MET cc_start: 0.7090 (mmm) cc_final: 0.6846 (mmm) REVERT: A 699 GLN cc_start: 0.7780 (mm110) cc_final: 0.7543 (mp10) REVERT: A 738 LEU cc_start: 0.7659 (mt) cc_final: 0.7438 (mt) REVERT: A 879 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8148 (mmtt) REVERT: A 909 ASN cc_start: 0.7480 (t0) cc_final: 0.7260 (t0) REVERT: A 1004 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 29 LYS cc_start: 0.8291 (mttp) cc_final: 0.8024 (mttm) REVERT: C 72 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: C 111 THR cc_start: 0.8950 (t) cc_final: 0.8677 (m) REVERT: C 139 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: C 143 ARG cc_start: 0.7858 (ttp-170) cc_final: 0.7507 (ttp-110) outliers start: 9 outliers final: 2 residues processed: 138 average time/residue: 1.5162 time to fit residues: 222.3949 Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.125479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.087168 restraints weight = 11647.249| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.22 r_work: 0.2965 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9745 Z= 0.239 Angle : 0.498 5.417 13200 Z= 0.260 Chirality : 0.043 0.150 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.762 82.319 1311 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.89 % Allowed : 6.97 % Favored : 91.14 % 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: 1.22 (0.25), residues: 1200 helix: 1.50 (0.24), residues: 496 sheet: 1.03 (0.37), residues: 178 loop : 0.17 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 PHE 0.012 0.001 PHE A 237 TYR 0.014 0.001 TYR C 145 ARG 0.006 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8760 (mmp) cc_final: 0.8372 (mmp) REVERT: A 216 LYS cc_start: 0.7360 (mtmm) cc_final: 0.7007 (mttp) REVERT: A 250 TYR cc_start: 0.7588 (m-80) cc_final: 0.7081 (m-80) REVERT: A 262 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8592 (tmtp) REVERT: A 274 ASP cc_start: 0.7786 (t0) cc_final: 0.7202 (p0) REVERT: A 286 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8234 (mmp) REVERT: A 333 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8408 (mp10) REVERT: A 406 ARG cc_start: 0.8019 (mtm180) cc_final: 0.6831 (mtp85) REVERT: A 516 GLU cc_start: 0.8348 (mp0) cc_final: 0.7996 (pm20) REVERT: A 540 GLU cc_start: 0.7733 (tt0) cc_final: 0.7274 (mp0) REVERT: A 583 GLN cc_start: 0.8126 (mt0) cc_final: 0.7354 (mm110) REVERT: A 611 ASP cc_start: 0.7817 (m-30) cc_final: 0.7571 (m-30) REVERT: A 626 MET cc_start: 0.7297 (ttt) cc_final: 0.6882 (mpt) REVERT: A 668 MET cc_start: 0.7511 (mmm) cc_final: 0.7282 (mmm) REVERT: A 699 GLN cc_start: 0.7913 (mm110) cc_final: 0.7646 (mp10) REVERT: A 909 ASN cc_start: 0.7427 (t0) cc_final: 0.7133 (t0) REVERT: C 139 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.7103 (ttm-80) REVERT: C 143 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7323 (ttp-170) outliers start: 20 outliers final: 10 residues processed: 130 average time/residue: 1.4528 time to fit residues: 201.4164 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 80 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.087976 restraints weight = 11759.785| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.23 r_work: 0.2975 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9745 Z= 0.203 Angle : 0.474 5.386 13200 Z= 0.247 Chirality : 0.042 0.151 1471 Planarity : 0.004 0.043 1709 Dihedral : 5.296 71.433 1311 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.32 % Allowed : 8.95 % Favored : 89.73 % 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: 1.36 (0.25), residues: 1200 helix: 1.63 (0.24), residues: 489 sheet: 1.05 (0.38), residues: 178 loop : 0.26 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.000 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR C 74 ARG 0.007 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8719 (mmp) cc_final: 0.8393 (mmp) REVERT: A 216 LYS cc_start: 0.7350 (mtmm) cc_final: 0.6983 (mttp) REVERT: A 250 TYR cc_start: 0.7576 (m-80) cc_final: 0.7117 (m-80) REVERT: A 262 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8585 (tmtp) REVERT: A 274 ASP cc_start: 0.7780 (t0) cc_final: 0.7171 (p0) REVERT: A 286 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8232 (mmp) REVERT: A 333 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8386 (mp10) REVERT: A 406 ARG cc_start: 0.8010 (mtm180) cc_final: 0.6829 (mtp85) REVERT: A 516 GLU cc_start: 0.8365 (mp0) cc_final: 0.7986 (pm20) REVERT: A 540 GLU cc_start: 0.7722 (tt0) cc_final: 0.7244 (mp0) REVERT: A 583 GLN cc_start: 0.8203 (mt0) cc_final: 0.7360 (mm110) REVERT: A 611 ASP cc_start: 0.7778 (m-30) cc_final: 0.7529 (m-30) REVERT: A 626 MET cc_start: 0.7289 (ttt) cc_final: 0.6881 (mpt) REVERT: A 668 MET cc_start: 0.7490 (mmm) cc_final: 0.7251 (mmm) REVERT: A 699 GLN cc_start: 0.7925 (mm110) cc_final: 0.7657 (mp10) REVERT: A 909 ASN cc_start: 0.7389 (t0) cc_final: 0.7131 (t0) REVERT: B 71 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8642 (pp) REVERT: C 139 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.7098 (ttm-80) REVERT: C 143 ARG cc_start: 0.7652 (ttp-170) cc_final: 0.7328 (ttp-110) outliers start: 14 outliers final: 7 residues processed: 116 average time/residue: 1.5069 time to fit residues: 186.2855 Evaluate side-chains 115 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 32 optimal weight: 0.0050 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 chunk 118 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.3472 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.127002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091102 restraints weight = 11545.160| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.14 r_work: 0.3036 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9745 Z= 0.161 Angle : 0.452 5.399 13200 Z= 0.235 Chirality : 0.041 0.150 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.151 69.021 1311 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.51 % Allowed : 9.99 % Favored : 88.50 % 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: 1.45 (0.25), residues: 1200 helix: 1.71 (0.24), residues: 489 sheet: 1.09 (0.37), residues: 178 loop : 0.32 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.008 0.001 TYR C 145 ARG 0.008 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.128 Fit side-chains REVERT: A 196 MET cc_start: 0.8724 (mmp) cc_final: 0.8384 (mmp) REVERT: A 216 LYS cc_start: 0.7450 (mtmm) cc_final: 0.7082 (mttp) REVERT: A 250 TYR cc_start: 0.7596 (m-80) cc_final: 0.7178 (m-80) REVERT: A 262 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8635 (tmtp) REVERT: A 274 ASP cc_start: 0.7743 (t0) cc_final: 0.7172 (p0) REVERT: A 333 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8377 (mp10) REVERT: A 406 ARG cc_start: 0.8046 (mtm180) cc_final: 0.6867 (mtp85) REVERT: A 516 GLU cc_start: 0.8376 (mp0) cc_final: 0.8057 (pm20) REVERT: A 540 GLU cc_start: 0.7730 (tt0) cc_final: 0.7288 (mp0) REVERT: A 583 GLN cc_start: 0.8177 (mt0) cc_final: 0.7377 (mm110) REVERT: A 611 ASP cc_start: 0.7831 (m-30) cc_final: 0.7590 (m-30) REVERT: A 626 MET cc_start: 0.7343 (ttt) cc_final: 0.6923 (mpt) REVERT: A 668 MET cc_start: 0.7536 (mmm) cc_final: 0.7304 (mmm) REVERT: A 699 GLN cc_start: 0.7956 (mm110) cc_final: 0.7708 (mp10) REVERT: A 909 ASN cc_start: 0.7405 (t0) cc_final: 0.7143 (t0) REVERT: B 71 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8642 (pp) REVERT: C 139 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7155 (ttm-80) REVERT: C 143 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7331 (ttp-170) outliers start: 16 outliers final: 6 residues processed: 113 average time/residue: 1.6029 time to fit residues: 192.9060 Evaluate side-chains 109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 86 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 26 optimal weight: 0.0970 chunk 92 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 96 optimal weight: 0.0980 chunk 81 optimal weight: 0.0870 chunk 27 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.1156 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093052 restraints weight = 11640.236| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.21 r_work: 0.3057 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9745 Z= 0.117 Angle : 0.445 11.690 13200 Z= 0.228 Chirality : 0.040 0.160 1471 Planarity : 0.004 0.042 1709 Dihedral : 5.060 81.563 1310 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 11.12 % Favored : 87.56 % 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: 1.62 (0.25), residues: 1200 helix: 1.86 (0.24), residues: 489 sheet: 1.10 (0.37), residues: 185 loop : 0.43 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 669 HIS 0.002 0.000 HIS A 819 PHE 0.008 0.001 PHE A 237 TYR 0.007 0.001 TYR A 736 ARG 0.007 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.082 Fit side-chains REVERT: A 216 LYS cc_start: 0.7434 (mtmm) cc_final: 0.7063 (mttp) REVERT: A 250 TYR cc_start: 0.7594 (m-80) cc_final: 0.7173 (m-80) REVERT: A 262 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8710 (tmtp) REVERT: A 274 ASP cc_start: 0.7812 (t0) cc_final: 0.7177 (p0) REVERT: A 333 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8398 (mp10) REVERT: A 406 ARG cc_start: 0.8009 (mtm180) cc_final: 0.6824 (mtp85) REVERT: A 516 GLU cc_start: 0.8396 (mp0) cc_final: 0.8021 (pm20) REVERT: A 540 GLU cc_start: 0.7732 (tt0) cc_final: 0.7276 (mp0) REVERT: A 583 GLN cc_start: 0.8084 (mt0) cc_final: 0.7349 (mm110) REVERT: A 611 ASP cc_start: 0.7783 (m-30) cc_final: 0.7529 (m-30) REVERT: A 626 MET cc_start: 0.7329 (ttt) cc_final: 0.6909 (mpt) REVERT: A 668 MET cc_start: 0.7444 (mmm) cc_final: 0.7239 (mmm) REVERT: A 699 GLN cc_start: 0.7937 (mm110) cc_final: 0.7683 (mp10) REVERT: A 909 ASN cc_start: 0.7377 (t0) cc_final: 0.7125 (t0) REVERT: A 981 LYS cc_start: 0.8460 (mmtp) cc_final: 0.8122 (mtpp) REVERT: B 71 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 92 GLN cc_start: 0.7932 (mm-40) cc_final: 0.6954 (tm-30) REVERT: C 139 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.7133 (ttm-80) REVERT: C 143 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7377 (ttp-170) outliers start: 14 outliers final: 7 residues processed: 113 average time/residue: 1.4323 time to fit residues: 172.4408 Evaluate side-chains 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.125218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089086 restraints weight = 11822.950| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.22 r_work: 0.2988 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9745 Z= 0.297 Angle : 0.509 11.128 13200 Z= 0.262 Chirality : 0.044 0.163 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.326 88.032 1310 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.41 % Allowed : 11.78 % 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: 1.42 (0.24), residues: 1200 helix: 1.66 (0.24), residues: 490 sheet: 1.06 (0.37), residues: 180 loop : 0.34 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 608 HIS 0.003 0.001 HIS A 29 PHE 0.013 0.002 PHE A 237 TYR 0.010 0.001 TYR A 544 ARG 0.008 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.169 Fit side-chains REVERT: A 216 LYS cc_start: 0.7368 (mtmm) cc_final: 0.6972 (mttp) REVERT: A 250 TYR cc_start: 0.7644 (m-80) cc_final: 0.7183 (m-80) REVERT: A 262 LYS cc_start: 0.8959 (ttpp) cc_final: 0.8685 (tmtp) REVERT: A 274 ASP cc_start: 0.7770 (t0) cc_final: 0.7168 (p0) REVERT: A 333 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8392 (mp10) REVERT: A 406 ARG cc_start: 0.8043 (mtm180) cc_final: 0.6853 (mtp85) REVERT: A 516 GLU cc_start: 0.8401 (mp0) cc_final: 0.7993 (pm20) REVERT: A 540 GLU cc_start: 0.7803 (tt0) cc_final: 0.7291 (mp0) REVERT: A 583 GLN cc_start: 0.8201 (mt0) cc_final: 0.7371 (mm110) REVERT: A 611 ASP cc_start: 0.7862 (m-30) cc_final: 0.7646 (m-30) REVERT: A 626 MET cc_start: 0.7354 (ttt) cc_final: 0.6946 (mpt) REVERT: A 699 GLN cc_start: 0.7951 (mm110) cc_final: 0.7681 (mp10) REVERT: A 909 ASN cc_start: 0.7382 (t0) cc_final: 0.7113 (t0) REVERT: A 981 LYS cc_start: 0.8472 (mmtp) cc_final: 0.8106 (mtpp) REVERT: C 139 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: C 143 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7466 (ttp-170) outliers start: 15 outliers final: 8 residues processed: 114 average time/residue: 1.4856 time to fit residues: 180.2484 Evaluate side-chains 110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 0.0040 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.127142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091110 restraints weight = 11763.624| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.17 r_work: 0.3015 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9745 Z= 0.162 Angle : 0.457 10.240 13200 Z= 0.236 Chirality : 0.041 0.154 1471 Planarity : 0.004 0.043 1709 Dihedral : 5.236 89.674 1310 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.23 % Allowed : 11.97 % 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: 1.53 (0.25), residues: 1200 helix: 1.73 (0.24), residues: 495 sheet: 1.04 (0.37), residues: 187 loop : 0.43 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS A 721 PHE 0.009 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.008 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.088 Fit side-chains REVERT: A 216 LYS cc_start: 0.7310 (mtmm) cc_final: 0.6922 (mttp) REVERT: A 250 TYR cc_start: 0.7595 (m-80) cc_final: 0.7182 (m-80) REVERT: A 262 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8668 (tmtp) REVERT: A 274 ASP cc_start: 0.7767 (t0) cc_final: 0.7121 (p0) REVERT: A 406 ARG cc_start: 0.7968 (mtm180) cc_final: 0.6769 (mtp85) REVERT: A 516 GLU cc_start: 0.8371 (mp0) cc_final: 0.7971 (pm20) REVERT: A 540 GLU cc_start: 0.7699 (tt0) cc_final: 0.7191 (mp0) REVERT: A 583 GLN cc_start: 0.8069 (mt0) cc_final: 0.7286 (mm110) REVERT: A 611 ASP cc_start: 0.7795 (m-30) cc_final: 0.7561 (m-30) REVERT: A 626 MET cc_start: 0.7293 (ttt) cc_final: 0.6885 (mpt) REVERT: A 699 GLN cc_start: 0.7909 (mm110) cc_final: 0.7640 (mp10) REVERT: A 909 ASN cc_start: 0.7336 (t0) cc_final: 0.7075 (t0) REVERT: A 981 LYS cc_start: 0.8435 (mmtp) cc_final: 0.8067 (mtpp) REVERT: B 71 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8601 (pp) REVERT: C 143 ARG cc_start: 0.7698 (ttp-170) cc_final: 0.7418 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 1.4338 time to fit residues: 174.6676 Evaluate side-chains 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.126724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088681 restraints weight = 11736.739| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.22 r_work: 0.2983 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9745 Z= 0.198 Angle : 0.468 10.288 13200 Z= 0.241 Chirality : 0.042 0.151 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.232 88.411 1310 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.51 % Allowed : 11.88 % Favored : 86.62 % 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: 1.53 (0.25), residues: 1200 helix: 1.70 (0.24), residues: 496 sheet: 1.08 (0.37), residues: 186 loop : 0.44 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.001 0.000 HIS C 125 PHE 0.010 0.001 PHE A 237 TYR 0.007 0.001 TYR A 150 ARG 0.008 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.112 Fit side-chains REVERT: A 216 LYS cc_start: 0.7348 (mtmm) cc_final: 0.6956 (mttp) REVERT: A 250 TYR cc_start: 0.7557 (m-80) cc_final: 0.7159 (m-80) REVERT: A 262 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8687 (tmtp) REVERT: A 274 ASP cc_start: 0.7792 (t0) cc_final: 0.7150 (p0) REVERT: A 406 ARG cc_start: 0.7999 (mtm180) cc_final: 0.6810 (mtp85) REVERT: A 516 GLU cc_start: 0.8385 (mp0) cc_final: 0.7991 (pm20) REVERT: A 540 GLU cc_start: 0.7694 (tt0) cc_final: 0.7218 (mp0) REVERT: A 583 GLN cc_start: 0.8101 (mt0) cc_final: 0.7320 (mm110) REVERT: A 611 ASP cc_start: 0.7791 (m-30) cc_final: 0.7554 (m-30) REVERT: A 626 MET cc_start: 0.7336 (ttt) cc_final: 0.6932 (mpt) REVERT: A 699 GLN cc_start: 0.7943 (mm110) cc_final: 0.7673 (mp10) REVERT: A 909 ASN cc_start: 0.7355 (t0) cc_final: 0.7094 (t0) REVERT: A 981 LYS cc_start: 0.8467 (mmtp) cc_final: 0.8107 (mtpp) REVERT: B 71 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8639 (pp) REVERT: C 143 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7457 (ttp-170) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 1.4471 time to fit residues: 177.7426 Evaluate side-chains 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.126155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.090067 restraints weight = 11676.412| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.16 r_work: 0.3019 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9745 Z= 0.242 Angle : 0.491 9.829 13200 Z= 0.253 Chirality : 0.043 0.151 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.223 81.632 1310 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.51 % Allowed : 11.97 % Favored : 86.52 % 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: 1.47 (0.25), residues: 1200 helix: 1.72 (0.24), residues: 490 sheet: 1.07 (0.37), residues: 180 loop : 0.35 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 PHE 0.011 0.001 PHE A 237 TYR 0.016 0.001 TYR C 145 ARG 0.008 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.141 Fit side-chains REVERT: A 216 LYS cc_start: 0.7375 (mtmm) cc_final: 0.6983 (mttp) REVERT: A 250 TYR cc_start: 0.7446 (m-80) cc_final: 0.7102 (m-80) REVERT: A 262 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8671 (tmtp) REVERT: A 274 ASP cc_start: 0.7775 (t0) cc_final: 0.7167 (p0) REVERT: A 406 ARG cc_start: 0.8009 (mtm180) cc_final: 0.6846 (mtp85) REVERT: A 516 GLU cc_start: 0.8402 (mp0) cc_final: 0.8007 (pm20) REVERT: A 540 GLU cc_start: 0.7809 (tt0) cc_final: 0.7312 (mp0) REVERT: A 583 GLN cc_start: 0.8135 (mt0) cc_final: 0.7340 (mm110) REVERT: A 611 ASP cc_start: 0.7863 (m-30) cc_final: 0.7646 (m-30) REVERT: A 626 MET cc_start: 0.7324 (ttt) cc_final: 0.6925 (mpt) REVERT: A 699 GLN cc_start: 0.7957 (mm110) cc_final: 0.7700 (mp10) REVERT: A 909 ASN cc_start: 0.7385 (t0) cc_final: 0.7116 (t0) REVERT: A 981 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8114 (mtpp) REVERT: B 71 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8665 (pp) REVERT: C 143 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7476 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.4019 time to fit residues: 173.5602 Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.126434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.088299 restraints weight = 11816.144| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.23 r_work: 0.2978 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.003 0.033 9745 Z= 0.216 Angle : 0.487 10.107 13200 Z= 0.250 Chirality : 0.042 0.152 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.241 83.381 1310 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 12.54 % Favored : 86.15 % 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: 1.46 (0.25), residues: 1200 helix: 1.64 (0.24), residues: 496 sheet: 1.09 (0.37), residues: 180 loop : 0.39 (0.28), residues: 524 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 0.011 0.001 PHE A 237 TYR 0.015 0.001 TYR C 145 ARG 0.009 0.000 ARG C 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.050 Fit side-chains REVERT: A 216 LYS cc_start: 0.7334 (mtmm) cc_final: 0.6937 (mttp) REVERT: A 250 TYR cc_start: 0.7417 (m-80) cc_final: 0.7065 (m-80) REVERT: A 262 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8626 (tmtp) REVERT: A 274 ASP cc_start: 0.7783 (t0) cc_final: 0.7135 (p0) REVERT: A 406 ARG cc_start: 0.7972 (mtm180) cc_final: 0.6802 (mtp85) REVERT: A 516 GLU cc_start: 0.8381 (mp0) cc_final: 0.7993 (pm20) REVERT: A 540 GLU cc_start: 0.7704 (tt0) cc_final: 0.7218 (mp0) REVERT: A 583 GLN cc_start: 0.8099 (mt0) cc_final: 0.7315 (mm110) REVERT: A 611 ASP cc_start: 0.7804 (m-30) cc_final: 0.7577 (m-30) REVERT: A 626 MET cc_start: 0.7326 (ttt) cc_final: 0.6924 (mpt) REVERT: A 699 GLN cc_start: 0.7948 (mm110) cc_final: 0.7680 (mp10) REVERT: A 909 ASN cc_start: 0.7360 (t0) cc_final: 0.7094 (t0) REVERT: A 981 LYS cc_start: 0.8467 (mmtp) cc_final: 0.8101 (mtpp) REVERT: B 71 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8641 (pp) REVERT: C 143 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7477 (ttp-170) outliers start: 14 outliers final: 11 residues processed: 116 average time/residue: 1.4293 time to fit residues: 176.4954 Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.125925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089989 restraints weight = 11731.738| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.20 r_work: 0.3009 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9745 Z= 0.250 Angle : 0.499 10.164 13200 Z= 0.256 Chirality : 0.043 0.153 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.326 87.279 1310 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.23 % Allowed : 12.91 % Favored : 85.86 % 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 (0.24), residues: 1200 helix: 1.60 (0.24), residues: 496 sheet: 1.05 (0.37), residues: 180 loop : 0.38 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 125 PHE 0.011 0.001 PHE A 237 TYR 0.017 0.001 TYR C 145 ARG 0.009 0.000 ARG C 8 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7253.78 seconds wall clock time: 129 minutes 5.13 seconds (7745.13 seconds total)