Starting phenix.real_space_refine on Sun Aug 4 04:02:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5j_44214/08_2024/9b5j_44214.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5j_44214/08_2024/9b5j_44214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5j_44214/08_2024/9b5j_44214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5j_44214/08_2024/9b5j_44214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5j_44214/08_2024/9b5j_44214.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5j_44214/08_2024/9b5j_44214.cif" } resolution = 2.86 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= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 360": "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: 9525 Number of models: 1 Model: "" Number of chains: 6 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: "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: 7.02, per 1000 atoms: 0.74 Number of scatterers: 9525 At special positions: 0 Unit cell: (82.992, 97.888, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 1 15.00 O 1829 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=2.93 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 1.8 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: 50 helices and 9 sheets defined 46.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.759A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.787A pdb=" N MET A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.596A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.892A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.369A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.527A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 123 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.697A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 4.032A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.286A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.625A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.978A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.577A 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 479 through 483 removed outlier: 3.678A pdb=" N VAL A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) 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: 4.001A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.888A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.628A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.518A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.986A 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 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.556A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.817A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.557A 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 752 removed outlier: 3.846A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.622A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (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 850 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.678A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.837A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain '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 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.739A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.334A 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: 4.290A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.367A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA6, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.402A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.402A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.839A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.635A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1230 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: 4.40 Time building geometry restraints manager: 4.88 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: 5697 1.54 - 1.67: 66 1.67 - 1.81: 64 Bond restraints: 9737 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 1.34e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C VAL A 949 " pdb=" O VAL A 949 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.24e+00 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 9.32e-01 ... (remaining 9732 not shown) Histogram of bond angle deviations from ideal: 100.12 - 115.94: 6388 115.94 - 131.76: 6788 131.76 - 147.59: 10 147.59 - 163.41: 0 163.41 - 179.23: 1 Bond angle restraints: 13187 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 121.70 128.22 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.66 4.24 1.50e+00 4.44e-01 7.98e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.60 112.37 7.23 3.00e+00 1.11e-01 5.82e+00 angle pdb=" C4' AMP B 101 " pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " ideal model delta sigma weight residual 111.70 108.35 3.35 1.50e+00 4.44e-01 4.99e+00 angle pdb=" N ASP A 813 " pdb=" CA ASP A 813 " pdb=" CB ASP A 813 " ideal model delta sigma weight residual 113.65 111.05 2.60 1.47e+00 4.63e-01 3.13e+00 ... (remaining 13182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5671 17.81 - 35.63: 185 35.63 - 53.44: 38 53.44 - 71.26: 8 71.26 - 89.07: 3 Dihedral angle restraints: 5905 sinusoidal: 2399 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 -136.30 50.30 1 1.00e+01 1.00e-02 3.47e+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 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" N LEU A 115 " pdb=" CA LEU A 115 " pdb=" CB LEU A 115 " pdb=" CG LEU A 115 " ideal model delta sinusoidal sigma weight residual -60.00 -119.59 59.59 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 908 0.030 - 0.060: 410 0.060 - 0.091: 66 0.091 - 0.121: 72 0.121 - 0.151: 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 5.71e-01 chirality pdb=" CA ILE B 36 " pdb=" N ILE B 36 " pdb=" C ILE B 36 " pdb=" CB ILE B 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-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 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO C 95 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO C 121 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 90 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 91 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.014 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 250 2.71 - 3.26: 9335 3.26 - 3.80: 14628 3.80 - 4.35: 19624 4.35 - 4.90: 33842 Nonbonded interactions: 77679 Sorted by model distance: nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.161 3.040 nonbonded pdb=" ND2 ASN A 534 " pdb=" OE2 GLU A 558 " model vdw 2.235 3.120 nonbonded pdb=" OE1 GLU A 658 " pdb=" OH TYR A 732 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASP A 463 " pdb=" O2' AMP B 101 " model vdw 2.264 3.040 nonbonded pdb=" O GLU A 809 " pdb=" NE2 HIS A 819 " model vdw 2.269 3.120 ... (remaining 77674 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.860 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.004 0.073 9737 Z= 0.234 Angle : 0.461 7.234 13187 Z= 0.232 Chirality : 0.040 0.151 1471 Planarity : 0.003 0.034 1709 Dihedral : 9.887 89.073 3638 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.04 % Allowed : 2.83 % Favored : 96.14 % 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: 1.00 (0.25), residues: 1200 helix: 1.59 (0.25), residues: 496 sheet: 0.29 (0.37), residues: 189 loop : -0.02 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.009 0.001 PHE A 237 TYR 0.009 0.001 TYR A 544 ARG 0.002 0.000 ARG A 409 *********************** 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 142 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8001 (pt0) cc_final: 0.7762 (mp10) REVERT: A 196 MET cc_start: 0.8737 (mmp) cc_final: 0.8453 (mmm) REVERT: A 540 GLU cc_start: 0.7472 (tt0) cc_final: 0.7266 (mp0) REVERT: A 583 GLN cc_start: 0.8129 (mt0) cc_final: 0.7261 (mm-40) REVERT: A 614 GLU cc_start: 0.7511 (tp30) cc_final: 0.6492 (tm-30) REVERT: A 619 GLN cc_start: 0.7466 (tp40) cc_final: 0.6890 (tm-30) REVERT: A 811 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5524 (tp30) REVERT: A 840 ASP cc_start: 0.7768 (p0) cc_final: 0.7459 (p0) REVERT: A 879 LYS cc_start: 0.8373 (mttm) cc_final: 0.8092 (mttm) REVERT: B 51 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8118 (mt-10) REVERT: C 32 HIS cc_start: 0.7849 (t-170) cc_final: 0.7533 (t70) REVERT: C 72 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8237 (mmm-85) REVERT: C 140 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7303 (tm-30) outliers start: 11 outliers final: 2 residues processed: 142 average time/residue: 1.5861 time to fit residues: 238.2233 Evaluate side-chains 98 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 811 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: 0.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 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: 0.7477 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9737 Z= 0.272 Angle : 0.529 5.720 13187 Z= 0.274 Chirality : 0.043 0.158 1471 Planarity : 0.004 0.043 1709 Dihedral : 5.774 79.296 1308 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.60 % Allowed : 8.11 % Favored : 90.29 % 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: 0.98 (0.25), residues: 1200 helix: 1.43 (0.24), residues: 503 sheet: 0.65 (0.37), residues: 186 loop : -0.03 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.007 0.001 HIS A 819 PHE 0.013 0.001 PHE A1007 TYR 0.010 0.001 TYR A 834 ARG 0.005 0.001 ARG B 74 *********************** 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 123 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.7997 (pt0) cc_final: 0.7773 (mp10) REVERT: A 196 MET cc_start: 0.8743 (mmp) cc_final: 0.8513 (mmm) REVERT: A 469 LYS cc_start: 0.8370 (mppt) cc_final: 0.8141 (mmtm) REVERT: A 540 GLU cc_start: 0.7495 (tt0) cc_final: 0.7276 (mp0) REVERT: A 583 GLN cc_start: 0.8162 (mt0) cc_final: 0.7269 (mm-40) REVERT: A 614 GLU cc_start: 0.7199 (tp30) cc_final: 0.6372 (tm-30) REVERT: A 619 GLN cc_start: 0.7315 (tp40) cc_final: 0.6711 (tm-30) REVERT: A 840 ASP cc_start: 0.7546 (p0) cc_final: 0.7225 (p0) REVERT: A 913 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7039 (mp) REVERT: B 51 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 60 ASN cc_start: 0.8708 (m-40) cc_final: 0.8398 (t0) REVERT: C 32 HIS cc_start: 0.7798 (t-170) cc_final: 0.7481 (t70) REVERT: C 72 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: C 140 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7380 (tm-30) outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 1.4406 time to fit residues: 177.8816 Evaluate side-chains 105 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7470 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9737 Z= 0.214 Angle : 0.483 6.080 13187 Z= 0.250 Chirality : 0.042 0.152 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.323 73.276 1305 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 8.95 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1200 helix: 1.42 (0.24), residues: 503 sheet: 0.78 (0.38), residues: 184 loop : -0.04 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 819 PHE 0.011 0.001 PHE A 237 TYR 0.015 0.001 TYR A 250 ARG 0.005 0.000 ARG A 841 *********************** 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 122 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.7999 (pt0) cc_final: 0.7768 (mp-120) REVERT: A 196 MET cc_start: 0.8728 (mmp) cc_final: 0.8527 (mmm) REVERT: A 216 LYS cc_start: 0.7171 (pttm) cc_final: 0.6856 (pptt) REVERT: A 235 TYR cc_start: 0.8169 (m-80) cc_final: 0.7945 (m-80) REVERT: A 540 GLU cc_start: 0.7485 (tt0) cc_final: 0.7277 (mp0) REVERT: A 583 GLN cc_start: 0.8184 (mt0) cc_final: 0.7282 (mm-40) REVERT: A 614 GLU cc_start: 0.7201 (tp30) cc_final: 0.6359 (tm-30) REVERT: A 619 GLN cc_start: 0.7291 (tp40) cc_final: 0.6680 (tm-30) REVERT: A 840 ASP cc_start: 0.7436 (p0) cc_final: 0.7108 (p0) REVERT: A 913 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7085 (mp) REVERT: B 51 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 60 ASN cc_start: 0.8689 (m-40) cc_final: 0.8408 (t0) REVERT: C 32 HIS cc_start: 0.7829 (t-170) cc_final: 0.7487 (t70) REVERT: C 72 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8293 (mmm-85) REVERT: C 101 LYS cc_start: 0.8656 (mptp) cc_final: 0.8336 (mmtp) outliers start: 18 outliers final: 7 residues processed: 115 average time/residue: 1.3318 time to fit residues: 163.7795 Evaluate side-chains 107 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 913 ILE 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 106 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7486 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9737 Z= 0.293 Angle : 0.506 6.470 13187 Z= 0.261 Chirality : 0.043 0.147 1471 Planarity : 0.004 0.048 1709 Dihedral : 5.267 63.673 1305 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 9.99 % Favored : 88.31 % 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: 0.95 (0.25), residues: 1200 helix: 1.39 (0.24), residues: 503 sheet: 0.70 (0.38), residues: 185 loop : -0.07 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 819 PHE 0.012 0.001 PHE A 237 TYR 0.012 0.001 TYR A 250 ARG 0.004 0.000 ARG A 841 *********************** 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 117 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8013 (pt0) cc_final: 0.7772 (mp-120) REVERT: A 196 MET cc_start: 0.8747 (mmp) cc_final: 0.8484 (mmm) REVERT: A 235 TYR cc_start: 0.8252 (m-80) cc_final: 0.8041 (m-80) REVERT: A 540 GLU cc_start: 0.7489 (tt0) cc_final: 0.7271 (mp0) REVERT: A 583 GLN cc_start: 0.8198 (mt0) cc_final: 0.7285 (mm-40) REVERT: A 614 GLU cc_start: 0.7258 (tp30) cc_final: 0.6458 (tm-30) REVERT: A 619 GLN cc_start: 0.7219 (tp40) cc_final: 0.6576 (tm-30) REVERT: A 840 ASP cc_start: 0.7466 (p0) cc_final: 0.7146 (p0) REVERT: A 913 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7023 (mp) REVERT: B 51 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8081 (mt-10) REVERT: B 60 ASN cc_start: 0.8650 (m-40) cc_final: 0.8373 (t0) REVERT: C 32 HIS cc_start: 0.7838 (t-170) cc_final: 0.7498 (t70) REVERT: C 72 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8320 (mmm-85) REVERT: C 101 LYS cc_start: 0.8664 (mptp) cc_final: 0.8346 (mmtp) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 1.3807 time to fit residues: 165.0560 Evaluate side-chains 106 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.0000 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 overall best weight: 0.4382 ------------------------------------------------------------------------------- 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: 0.7465 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9737 Z= 0.177 Angle : 0.480 11.787 13187 Z= 0.244 Chirality : 0.041 0.157 1471 Planarity : 0.004 0.048 1709 Dihedral : 5.184 62.351 1305 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 10.84 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1200 helix: 1.51 (0.24), residues: 503 sheet: 0.71 (0.38), residues: 187 loop : 0.02 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.010 0.001 PHE A 237 TYR 0.009 0.001 TYR C 74 ARG 0.006 0.000 ARG A 841 *********************** 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 118 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.106 Fit side-chains REVERT: A 105 GLN cc_start: 0.8009 (pt0) cc_final: 0.7760 (mp-120) REVERT: A 216 LYS cc_start: 0.7253 (pttm) cc_final: 0.6876 (pptt) REVERT: A 221 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7743 (tp) REVERT: A 235 TYR cc_start: 0.8249 (m-80) cc_final: 0.7992 (m-80) REVERT: A 540 GLU cc_start: 0.7451 (tt0) cc_final: 0.7246 (mp0) REVERT: A 583 GLN cc_start: 0.8208 (mt0) cc_final: 0.7305 (mm-40) REVERT: A 614 GLU cc_start: 0.7241 (tp30) cc_final: 0.6443 (tm-30) REVERT: A 619 GLN cc_start: 0.7197 (tp40) cc_final: 0.6581 (tm-30) REVERT: A 811 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5922 (tp30) REVERT: A 840 ASP cc_start: 0.7467 (p0) cc_final: 0.7131 (p0) REVERT: A 913 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7073 (mp) REVERT: B 51 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 60 ASN cc_start: 0.8593 (m-40) cc_final: 0.8327 (t0) REVERT: C 32 HIS cc_start: 0.7827 (t-170) cc_final: 0.7489 (t70) REVERT: C 72 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8302 (mmm-85) outliers start: 19 outliers final: 7 residues processed: 114 average time/residue: 1.4284 time to fit residues: 173.7583 Evaluate side-chains 107 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.0070 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.3314 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9737 Z= 0.155 Angle : 0.484 11.481 13187 Z= 0.245 Chirality : 0.041 0.202 1471 Planarity : 0.004 0.047 1709 Dihedral : 5.034 69.114 1304 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 12.16 % 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: 1.16 (0.25), residues: 1200 helix: 1.57 (0.24), residues: 504 sheet: 0.79 (0.38), residues: 187 loop : 0.04 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.010 0.001 PHE A 842 TYR 0.020 0.001 TYR C 127 ARG 0.010 0.000 ARG A 841 *********************** 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 112 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.093 Fit side-chains REVERT: A 105 GLN cc_start: 0.8018 (pt0) cc_final: 0.7769 (mp-120) REVERT: A 216 LYS cc_start: 0.7276 (pttm) cc_final: 0.6922 (pptt) REVERT: A 221 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 583 GLN cc_start: 0.8218 (mt0) cc_final: 0.7310 (mm-40) REVERT: A 614 GLU cc_start: 0.7230 (tp30) cc_final: 0.6444 (tm-30) REVERT: A 619 GLN cc_start: 0.7184 (tp40) cc_final: 0.6553 (tm-30) REVERT: A 840 ASP cc_start: 0.7431 (p0) cc_final: 0.7103 (p0) REVERT: B 51 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8084 (mt-10) REVERT: B 60 ASN cc_start: 0.8598 (m-40) cc_final: 0.8343 (t0) REVERT: C 32 HIS cc_start: 0.7818 (t-170) cc_final: 0.7482 (t70) REVERT: C 72 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8299 (mmm-85) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 1.2766 time to fit residues: 149.0314 Evaluate side-chains 107 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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: 0.7461 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9737 Z= 0.198 Angle : 0.489 10.090 13187 Z= 0.249 Chirality : 0.042 0.195 1471 Planarity : 0.004 0.048 1709 Dihedral : 5.007 67.883 1304 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.04 % Allowed : 12.54 % Favored : 86.43 % 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: 1.68 (0.24), residues: 497 sheet: 0.80 (0.38), residues: 188 loop : 0.04 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.010 0.001 PHE A 237 TYR 0.020 0.001 TYR C 127 ARG 0.008 0.000 ARG A 841 *********************** 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 109 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.047 Fit side-chains REVERT: A 105 GLN cc_start: 0.8026 (pt0) cc_final: 0.7769 (mp-120) REVERT: A 216 LYS cc_start: 0.7174 (pttm) cc_final: 0.6821 (pptt) REVERT: A 221 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 583 GLN cc_start: 0.8229 (mt0) cc_final: 0.7313 (mm-40) REVERT: A 614 GLU cc_start: 0.7221 (tp30) cc_final: 0.6446 (tm-30) REVERT: A 619 GLN cc_start: 0.7188 (tp40) cc_final: 0.6554 (tm-30) REVERT: A 840 ASP cc_start: 0.7415 (p0) cc_final: 0.7094 (p0) REVERT: B 51 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8083 (mt-10) REVERT: B 60 ASN cc_start: 0.8605 (m-40) cc_final: 0.8351 (t0) REVERT: C 32 HIS cc_start: 0.7833 (t-170) cc_final: 0.7497 (t70) REVERT: C 72 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8301 (mmm-85) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 1.3081 time to fit residues: 151.3496 Evaluate side-chains 106 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7488 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9737 Z= 0.319 Angle : 0.539 11.376 13187 Z= 0.274 Chirality : 0.044 0.204 1471 Planarity : 0.004 0.049 1709 Dihedral : 5.218 71.655 1304 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.79 % Allowed : 11.78 % Favored : 86.43 % 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: 1.08 (0.25), residues: 1200 helix: 1.53 (0.24), residues: 497 sheet: 0.77 (0.38), residues: 187 loop : -0.02 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 818 PHE 0.012 0.002 PHE A1007 TYR 0.021 0.001 TYR C 127 ARG 0.008 0.000 ARG A 841 *********************** 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 118 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.021 Fit side-chains REVERT: A 105 GLN cc_start: 0.8019 (pt0) cc_final: 0.7770 (mp-120) REVERT: A 216 LYS cc_start: 0.7205 (pttm) cc_final: 0.6847 (pptt) REVERT: A 221 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7824 (tp) REVERT: A 583 GLN cc_start: 0.8234 (mt0) cc_final: 0.7314 (mm-40) REVERT: A 614 GLU cc_start: 0.7225 (tp30) cc_final: 0.6443 (tm-30) REVERT: A 619 GLN cc_start: 0.7462 (tp40) cc_final: 0.6745 (tm-30) REVERT: A 811 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5935 (tp30) REVERT: A 840 ASP cc_start: 0.7430 (p0) cc_final: 0.7118 (p0) REVERT: B 51 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8055 (mt-10) REVERT: B 60 ASN cc_start: 0.8615 (m-40) cc_final: 0.8372 (t0) REVERT: C 32 HIS cc_start: 0.7858 (t-170) cc_final: 0.7532 (t70) REVERT: C 72 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8340 (mmm-85) outliers start: 19 outliers final: 8 residues processed: 114 average time/residue: 1.3053 time to fit residues: 159.5171 Evaluate side-chains 101 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 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 106 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.0040 chunk 68 optimal weight: 0.7980 overall best weight: 0.3650 ------------------------------------------------------------------------------- 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: 0.7458 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9737 Z= 0.162 Angle : 0.487 10.195 13187 Z= 0.247 Chirality : 0.041 0.179 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.937 59.614 1304 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.94 % Allowed : 13.01 % Favored : 86.05 % 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: 1.21 (0.25), residues: 1200 helix: 1.65 (0.24), residues: 498 sheet: 0.84 (0.38), residues: 187 loop : 0.05 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.010 0.001 PHE A 842 TYR 0.020 0.001 TYR C 127 ARG 0.008 0.000 ARG A 841 *********************** 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 106 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.960 Fit side-chains REVERT: A 105 GLN cc_start: 0.8027 (pt0) cc_final: 0.7769 (mp-120) REVERT: A 216 LYS cc_start: 0.7181 (pttm) cc_final: 0.6849 (pptt) REVERT: A 221 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 583 GLN cc_start: 0.8224 (mt0) cc_final: 0.7311 (mm-40) REVERT: A 614 GLU cc_start: 0.7210 (tp30) cc_final: 0.6430 (tm-30) REVERT: A 619 GLN cc_start: 0.7443 (tp40) cc_final: 0.6743 (tm-30) REVERT: A 840 ASP cc_start: 0.7403 (p0) cc_final: 0.7081 (p0) REVERT: A 913 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6945 (mp) REVERT: B 51 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 60 ASN cc_start: 0.8603 (m-40) cc_final: 0.8354 (t0) REVERT: C 32 HIS cc_start: 0.7846 (t-170) cc_final: 0.7507 (t70) REVERT: C 72 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8330 (mmm-85) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 1.3539 time to fit residues: 154.3364 Evaluate side-chains 104 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 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 53 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 0.0470 chunk 74 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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: 0.7457 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9737 Z= 0.169 Angle : 0.487 9.923 13187 Z= 0.246 Chirality : 0.041 0.179 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.880 57.391 1304 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.85 % Allowed : 13.20 % Favored : 85.96 % 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: 1.25 (0.25), residues: 1200 helix: 1.69 (0.24), residues: 498 sheet: 0.83 (0.38), residues: 188 loop : 0.05 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.000 HIS A 819 PHE 0.010 0.001 PHE A 842 TYR 0.021 0.001 TYR C 127 ARG 0.007 0.000 ARG A 841 ********************** 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 104 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.034 Fit side-chains REVERT: A 105 GLN cc_start: 0.8023 (pt0) cc_final: 0.7768 (mp-120) REVERT: A 216 LYS cc_start: 0.7167 (pttm) cc_final: 0.6835 (pptt) REVERT: A 221 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7866 (tp) REVERT: A 333 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8455 (mm-40) REVERT: A 583 GLN cc_start: 0.8240 (mt0) cc_final: 0.7310 (mm-40) REVERT: A 614 GLU cc_start: 0.7175 (tp30) cc_final: 0.6425 (tm-30) REVERT: A 619 GLN cc_start: 0.7431 (tp40) cc_final: 0.6694 (tm-30) REVERT: A 840 ASP cc_start: 0.7389 (p0) cc_final: 0.7071 (p0) REVERT: B 51 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8045 (mt-10) REVERT: B 60 ASN cc_start: 0.8589 (m-40) cc_final: 0.8353 (t0) REVERT: C 32 HIS cc_start: 0.7833 (t-170) cc_final: 0.7500 (t70) REVERT: C 72 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8325 (mmm-85) outliers start: 9 outliers final: 7 residues processed: 104 average time/residue: 1.3294 time to fit residues: 147.8705 Evaluate side-chains 103 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 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 87 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.0000 overall best weight: 0.3362 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.135221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094735 restraints weight = 11974.673| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.46 r_work: 0.2964 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9737 Z= 0.155 Angle : 0.478 9.494 13187 Z= 0.242 Chirality : 0.041 0.166 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.751 57.460 1304 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.94 % Allowed : 13.10 % Favored : 85.96 % 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: 1.30 (0.25), residues: 1200 helix: 1.73 (0.24), residues: 498 sheet: 0.87 (0.38), residues: 188 loop : 0.08 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.010 0.001 PHE A 842 TYR 0.020 0.001 TYR C 127 ARG 0.008 0.000 ARG A 841 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3635.05 seconds wall clock time: 63 minutes 51.23 seconds (3831.23 seconds total)