Starting phenix.real_space_refine on Sun Aug 4 09:32:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5l_44216/08_2024/9b5l_44216.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5l_44216/08_2024/9b5l_44216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5l_44216/08_2024/9b5l_44216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5l_44216/08_2024/9b5l_44216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5l_44216/08_2024/9b5l_44216.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5l_44216/08_2024/9b5l_44216.cif" } resolution = 3.3 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= 0.054 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 43 5.16 5 C 6449 2.51 5 N 1678 2.21 5 O 1946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D TYR 59": "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: 10117 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: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} 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: 6.65, per 1000 atoms: 0.66 Number of scatterers: 10117 At special positions: 0 Unit cell: (91.504, 98.952, 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 43 16.00 P 1 15.00 O 1946 8.00 N 1678 7.00 C 6449 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=2.90 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: 3.81 Conformation dependent library (CDL) restraints added in 2.1 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 45.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 removed outlier: 3.769A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.769A 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: 3.602A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.033A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.215A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.632A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.728A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.276A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.564A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.005A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.567A 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: 4.046A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 4.068A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.568A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.872A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) 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 removed outlier: 3.579A pdb=" N SER A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 641 removed outlier: 4.076A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.672A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.772A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.548A 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: 3.889A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.636A 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 849 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: 3.995A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (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 helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.948A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.400A 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: 4.375A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.255A 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: 6.327A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.200A 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: 6.391A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.454A 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: 6.391A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.139A 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: 3.918A 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: 11.245A pdb=" N GLY C 24 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE C 31 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 26 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16 476 hydrogen bonds defined for protein. 1296 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: 3.53 Time building geometry restraints manager: 4.18 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: 1723 1.27 - 1.40: 2409 1.40 - 1.54: 5972 1.54 - 1.67: 165 1.67 - 1.80: 66 Bond restraints: 10335 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 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 2.62e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.87e-01 ... (remaining 10330 not shown) Histogram of bond angle deviations from ideal: 100.17 - 116.01: 6854 116.01 - 131.86: 7127 131.86 - 147.71: 10 147.71 - 163.56: 0 163.56 - 179.40: 1 Bond angle restraints: 13992 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 127.77 -6.07 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.54 4.36 1.50e+00 4.44e-01 8.46e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.60 112.75 6.85 3.00e+00 1.11e-01 5.21e+00 angle pdb=" C4' AMP B 101 " pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " ideal model delta sigma weight residual 111.70 108.67 3.03 1.50e+00 4.44e-01 4.07e+00 angle pdb=" CA TYR A 544 " pdb=" CB TYR A 544 " pdb=" CG TYR A 544 " ideal model delta sigma weight residual 113.90 110.33 3.57 1.80e+00 3.09e-01 3.94e+00 ... (remaining 13987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6005 17.81 - 35.62: 228 35.62 - 53.43: 33 53.43 - 71.24: 11 71.24 - 89.05: 5 Dihedral angle restraints: 6282 sinusoidal: 2561 harmonic: 3721 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 -155.12 69.12 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CA ASP D 52 " pdb=" CB ASP D 52 " pdb=" CG ASP D 52 " pdb=" OD1 ASP D 52 " ideal model delta sinusoidal sigma weight residual -30.00 -88.56 58.56 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.35 16.65 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 917 0.028 - 0.056: 448 0.056 - 0.083: 100 0.083 - 0.111: 74 0.111 - 0.139: 29 Chirality restraints: 1568 Sorted by residual: 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 4.82e-01 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 2.57 -0.14 2.00e-01 2.50e+01 4.80e-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 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 659 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 660 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 660 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 660 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 756 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO A 757 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 757 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 757 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 18 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.015 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 63 2.53 - 3.12: 7854 3.12 - 3.71: 14744 3.71 - 4.31: 20966 4.31 - 4.90: 36516 Nonbonded interactions: 80143 Sorted by model distance: nonbonded pdb=" OG SER A 395 " pdb=" OD1 ASP A 875 " model vdw 1.933 3.040 nonbonded pdb=" OE2 GLU C 9 " pdb=" OH TYR C 60 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" OD2 ASP A 387 " model vdw 2.127 3.040 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.149 3.040 nonbonded pdb=" OG SER A 488 " pdb=" OE1 GLU A 489 " model vdw 2.199 3.040 ... (remaining 80138 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 75) selection = (chain 'D' and resid 1 through 75) } 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: 3.150 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.072 10335 Z= 0.266 Angle : 0.485 6.846 13992 Z= 0.251 Chirality : 0.040 0.139 1568 Planarity : 0.003 0.029 1812 Dihedral : 10.247 89.049 3875 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.42 % Allowed : 4.16 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.25), residues: 1273 helix: 1.95 (0.25), residues: 505 sheet: 0.53 (0.36), residues: 213 loop : 0.28 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 141 HIS 0.003 0.001 HIS A 458 PHE 0.011 0.001 PHE A 431 TYR 0.012 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) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8228 (mptt) cc_final: 0.7764 (tmtt) REVERT: A 35 MET cc_start: 0.8246 (ttp) cc_final: 0.7978 (ttp) REVERT: A 80 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8281 (tp40) REVERT: A 229 VAL cc_start: 0.9280 (t) cc_final: 0.8925 (p) REVERT: A 464 MET cc_start: 0.8778 (pmt) cc_final: 0.8513 (pmm) REVERT: A 474 ARG cc_start: 0.7667 (ptt-90) cc_final: 0.7382 (ptt180) REVERT: A 587 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8480 (tt0) REVERT: A 623 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6951 (t0) REVERT: A 718 ASN cc_start: 0.8622 (t0) cc_final: 0.8306 (t0) REVERT: A 748 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8537 (pt0) REVERT: A 821 ASP cc_start: 0.9004 (t70) cc_final: 0.8793 (t0) REVERT: A 885 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8601 (m-40) REVERT: B 18 GLU cc_start: 0.8756 (mp0) cc_final: 0.8220 (mp0) REVERT: C 34 GLN cc_start: 0.8767 (tt0) cc_final: 0.7998 (pp30) REVERT: C 66 LYS cc_start: 0.8557 (mttt) cc_final: 0.8283 (mtpt) REVERT: C 72 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8635 (mtp85) REVERT: C 92 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8254 (mm-40) REVERT: C 120 VAL cc_start: 0.8842 (t) cc_final: 0.8571 (m) REVERT: C 137 SER cc_start: 0.9062 (m) cc_final: 0.8775 (p) REVERT: D 31 GLN cc_start: 0.8172 (tt0) cc_final: 0.7599 (tp40) outliers start: 16 outliers final: 7 residues processed: 205 average time/residue: 0.2864 time to fit residues: 76.6644 Evaluate side-chains 132 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.7915 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10335 Z= 0.329 Angle : 0.593 6.912 13992 Z= 0.307 Chirality : 0.044 0.141 1568 Planarity : 0.004 0.050 1812 Dihedral : 6.593 89.367 1401 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.01 % Allowed : 7.79 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.24), residues: 1273 helix: 1.68 (0.24), residues: 515 sheet: 0.63 (0.37), residues: 212 loop : 0.12 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 141 HIS 0.008 0.001 HIS D 68 PHE 0.013 0.001 PHE A 633 TYR 0.021 0.002 TYR C 145 ARG 0.004 0.001 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8214 (mptt) cc_final: 0.7731 (tmtt) REVERT: A 35 MET cc_start: 0.8358 (ttp) cc_final: 0.8085 (ttp) REVERT: A 80 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7214 (tp40) REVERT: A 464 MET cc_start: 0.8756 (pmt) cc_final: 0.8469 (pmm) REVERT: A 474 ARG cc_start: 0.7870 (ptt-90) cc_final: 0.7513 (ptt180) REVERT: A 588 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7728 (mmmt) REVERT: A 623 ASN cc_start: 0.7187 (OUTLIER) cc_final: 0.6811 (t0) REVERT: A 717 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.8442 (t-90) REVERT: A 718 ASN cc_start: 0.8512 (t0) cc_final: 0.8065 (t0) REVERT: A 748 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8600 (pt0) REVERT: A 821 ASP cc_start: 0.9002 (t70) cc_final: 0.8786 (t0) REVERT: B 18 GLU cc_start: 0.8885 (mp0) cc_final: 0.8242 (mp0) REVERT: B 21 ASP cc_start: 0.8503 (m-30) cc_final: 0.7516 (m-30) REVERT: B 64 GLU cc_start: 0.9097 (mp0) cc_final: 0.8640 (mp0) REVERT: C 7 ASN cc_start: 0.8883 (t0) cc_final: 0.8602 (t0) REVERT: C 34 GLN cc_start: 0.8774 (tt0) cc_final: 0.8010 (pp30) REVERT: C 38 MET cc_start: 0.8312 (ppp) cc_final: 0.8065 (ppp) REVERT: C 66 LYS cc_start: 0.8557 (mttt) cc_final: 0.8307 (mtpt) REVERT: C 72 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8570 (mtp85) REVERT: C 92 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8280 (mm-40) REVERT: D 31 GLN cc_start: 0.8088 (tt0) cc_final: 0.7494 (tp40) REVERT: D 72 ARG cc_start: 0.7667 (tmm160) cc_final: 0.7153 (tmm160) outliers start: 34 outliers final: 25 residues processed: 158 average time/residue: 0.2714 time to fit residues: 58.3160 Evaluate side-chains 143 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10335 Z= 0.246 Angle : 0.525 6.133 13992 Z= 0.274 Chirality : 0.042 0.138 1568 Planarity : 0.004 0.037 1812 Dihedral : 6.417 87.640 1397 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.65 % Allowed : 9.47 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.24), residues: 1273 helix: 1.72 (0.24), residues: 517 sheet: 0.56 (0.36), residues: 216 loop : 0.02 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.015 0.001 HIS D 68 PHE 0.015 0.001 PHE A 633 TYR 0.016 0.001 TYR C 145 ARG 0.003 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8219 (mptt) cc_final: 0.7711 (tmtt) REVERT: A 35 MET cc_start: 0.8317 (ttp) cc_final: 0.8106 (ttp) REVERT: A 80 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8290 (tp40) REVERT: A 474 ARG cc_start: 0.7850 (ptt-90) cc_final: 0.7481 (ptt180) REVERT: A 507 THR cc_start: 0.9116 (m) cc_final: 0.8676 (p) REVERT: A 653 ASP cc_start: 0.8682 (m-30) cc_final: 0.7728 (m-30) REVERT: A 717 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8476 (t-90) REVERT: A 718 ASN cc_start: 0.8569 (t0) cc_final: 0.8105 (t0) REVERT: A 748 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8620 (pt0) REVERT: A 821 ASP cc_start: 0.9056 (t70) cc_final: 0.8810 (t0) REVERT: A 835 ASP cc_start: 0.8370 (m-30) cc_final: 0.8169 (m-30) REVERT: B 18 GLU cc_start: 0.8954 (mp0) cc_final: 0.8286 (mp0) REVERT: B 21 ASP cc_start: 0.8523 (m-30) cc_final: 0.7549 (m-30) REVERT: B 24 ASP cc_start: 0.8266 (m-30) cc_final: 0.7741 (p0) REVERT: B 64 GLU cc_start: 0.9087 (mp0) cc_final: 0.8657 (mp0) REVERT: C 34 GLN cc_start: 0.8781 (tt0) cc_final: 0.7856 (pp30) REVERT: C 38 MET cc_start: 0.8324 (ppp) cc_final: 0.8043 (ppp) REVERT: C 66 LYS cc_start: 0.8559 (mttt) cc_final: 0.8246 (mtpt) REVERT: C 72 ARG cc_start: 0.8846 (mmm-85) cc_final: 0.8608 (mtp85) REVERT: C 92 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8254 (mm-40) REVERT: D 31 GLN cc_start: 0.8052 (tt0) cc_final: 0.7514 (tp40) REVERT: D 72 ARG cc_start: 0.7631 (tmm160) cc_final: 0.7381 (tmm160) outliers start: 30 outliers final: 20 residues processed: 145 average time/residue: 0.2711 time to fit residues: 53.4236 Evaluate side-chains 134 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0470 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10335 Z= 0.148 Angle : 0.498 6.536 13992 Z= 0.258 Chirality : 0.041 0.143 1568 Planarity : 0.004 0.054 1812 Dihedral : 6.189 86.278 1395 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.57 % Allowed : 10.88 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.24), residues: 1273 helix: 1.81 (0.24), residues: 510 sheet: 0.74 (0.36), residues: 208 loop : 0.09 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.006 0.001 HIS D 68 PHE 0.026 0.001 PHE A 633 TYR 0.016 0.001 TYR C 145 ARG 0.008 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8166 (mptt) cc_final: 0.7647 (tmtt) REVERT: A 35 MET cc_start: 0.8337 (ttp) cc_final: 0.8111 (ttp) REVERT: A 51 GLU cc_start: 0.8459 (tp30) cc_final: 0.7979 (tp30) REVERT: A 464 MET cc_start: 0.8802 (pmm) cc_final: 0.8489 (pmm) REVERT: A 465 ASP cc_start: 0.8786 (t0) cc_final: 0.8528 (m-30) REVERT: A 474 ARG cc_start: 0.7847 (ptt-90) cc_final: 0.7364 (ptt90) REVERT: A 507 THR cc_start: 0.9132 (m) cc_final: 0.8728 (p) REVERT: A 558 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7754 (mm-30) REVERT: A 717 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8502 (t-90) REVERT: A 718 ASN cc_start: 0.8504 (t0) cc_final: 0.8023 (t0) REVERT: A 748 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8523 (pt0) REVERT: A 821 ASP cc_start: 0.9052 (t70) cc_final: 0.8787 (t0) REVERT: B 18 GLU cc_start: 0.8924 (mp0) cc_final: 0.8239 (mp0) REVERT: B 21 ASP cc_start: 0.8494 (m-30) cc_final: 0.7463 (m-30) REVERT: B 24 ASP cc_start: 0.8213 (m-30) cc_final: 0.7728 (p0) REVERT: B 64 GLU cc_start: 0.9078 (mp0) cc_final: 0.8715 (mp0) REVERT: C 34 GLN cc_start: 0.8770 (tt0) cc_final: 0.7847 (pp30) REVERT: C 38 MET cc_start: 0.8356 (ppp) cc_final: 0.8033 (ppp) REVERT: C 66 LYS cc_start: 0.8558 (mttt) cc_final: 0.8290 (mtpt) REVERT: C 72 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8595 (mtp85) REVERT: C 92 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8233 (mm-40) REVERT: D 18 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7940 (tm-30) REVERT: D 31 GLN cc_start: 0.8007 (tt0) cc_final: 0.7461 (tp40) REVERT: D 50 LEU cc_start: 0.7544 (mp) cc_final: 0.7237 (mp) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.2599 time to fit residues: 52.5408 Evaluate side-chains 136 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7903 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10335 Z= 0.219 Angle : 0.511 7.648 13992 Z= 0.263 Chirality : 0.042 0.160 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.771 88.748 1391 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.48 % Allowed : 11.33 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.24), residues: 1273 helix: 1.84 (0.24), residues: 509 sheet: 0.69 (0.36), residues: 208 loop : 0.11 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS D 68 PHE 0.014 0.001 PHE A 633 TYR 0.016 0.001 TYR A 250 ARG 0.003 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8188 (mptt) cc_final: 0.7662 (tmtt) REVERT: A 35 MET cc_start: 0.8342 (ttp) cc_final: 0.8106 (ttp) REVERT: A 51 GLU cc_start: 0.8556 (tp30) cc_final: 0.8296 (tp30) REVERT: A 465 ASP cc_start: 0.8797 (t0) cc_final: 0.8496 (m-30) REVERT: A 474 ARG cc_start: 0.7903 (ptt-90) cc_final: 0.7486 (ptt90) REVERT: A 507 THR cc_start: 0.9142 (m) cc_final: 0.8750 (p) REVERT: A 717 HIS cc_start: 0.8966 (OUTLIER) cc_final: 0.8471 (t-90) REVERT: A 718 ASN cc_start: 0.8500 (t0) cc_final: 0.8006 (t0) REVERT: A 748 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8534 (pt0) REVERT: A 818 HIS cc_start: 0.7472 (m90) cc_final: 0.7002 (m170) REVERT: A 821 ASP cc_start: 0.8970 (t70) cc_final: 0.8683 (t0) REVERT: B 18 GLU cc_start: 0.8952 (mp0) cc_final: 0.8151 (mp0) REVERT: B 21 ASP cc_start: 0.8550 (m-30) cc_final: 0.7335 (m-30) REVERT: B 24 ASP cc_start: 0.8240 (m-30) cc_final: 0.7761 (p0) REVERT: B 64 GLU cc_start: 0.9084 (mp0) cc_final: 0.8723 (mp0) REVERT: C 34 GLN cc_start: 0.8780 (tt0) cc_final: 0.7813 (pp30) REVERT: C 38 MET cc_start: 0.8368 (ppp) cc_final: 0.8021 (ppp) REVERT: C 66 LYS cc_start: 0.8585 (mttt) cc_final: 0.8273 (mtpt) REVERT: C 72 ARG cc_start: 0.8866 (mmm-85) cc_final: 0.8636 (mtp85) REVERT: C 92 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8216 (mm-40) REVERT: D 31 GLN cc_start: 0.8019 (tt0) cc_final: 0.7471 (tp40) outliers start: 28 outliers final: 19 residues processed: 132 average time/residue: 0.2606 time to fit residues: 47.6365 Evaluate side-chains 133 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.0470 chunk 117 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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: 0.7890 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10335 Z= 0.176 Angle : 0.494 5.734 13992 Z= 0.253 Chirality : 0.041 0.131 1568 Planarity : 0.003 0.040 1812 Dihedral : 5.648 87.593 1391 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.04 % Allowed : 12.12 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.24), residues: 1273 helix: 1.92 (0.24), residues: 503 sheet: 0.70 (0.38), residues: 196 loop : 0.05 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS D 68 PHE 0.012 0.001 PHE A 633 TYR 0.016 0.001 TYR C 145 ARG 0.003 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8179 (mptt) cc_final: 0.7641 (tmtt) REVERT: A 35 MET cc_start: 0.8332 (ttp) cc_final: 0.8107 (ttp) REVERT: A 51 GLU cc_start: 0.8521 (tp30) cc_final: 0.8037 (tp30) REVERT: A 465 ASP cc_start: 0.8783 (t0) cc_final: 0.8483 (m-30) REVERT: A 474 ARG cc_start: 0.7874 (ptt-90) cc_final: 0.7342 (ptt90) REVERT: A 507 THR cc_start: 0.9157 (m) cc_final: 0.8790 (p) REVERT: A 717 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8494 (t-90) REVERT: A 718 ASN cc_start: 0.8474 (t0) cc_final: 0.7955 (t0) REVERT: A 748 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8526 (pt0) REVERT: A 821 ASP cc_start: 0.8957 (t70) cc_final: 0.8690 (t0) REVERT: B 18 GLU cc_start: 0.8950 (mp0) cc_final: 0.8141 (mp0) REVERT: B 21 ASP cc_start: 0.8518 (m-30) cc_final: 0.7264 (m-30) REVERT: B 24 ASP cc_start: 0.8221 (m-30) cc_final: 0.7760 (p0) REVERT: B 64 GLU cc_start: 0.9080 (mp0) cc_final: 0.8717 (mp0) REVERT: C 34 GLN cc_start: 0.8780 (tt0) cc_final: 0.7812 (pp30) REVERT: C 38 MET cc_start: 0.8377 (ppp) cc_final: 0.8017 (ppp) REVERT: C 66 LYS cc_start: 0.8552 (mttt) cc_final: 0.8242 (mtpt) REVERT: C 72 ARG cc_start: 0.8872 (mmm-85) cc_final: 0.8492 (mtp85) REVERT: C 92 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8215 (mm-40) REVERT: D 31 GLN cc_start: 0.8003 (tt0) cc_final: 0.7448 (tp40) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.2701 time to fit residues: 50.6818 Evaluate side-chains 134 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10335 Z= 0.249 Angle : 0.526 8.635 13992 Z= 0.270 Chirality : 0.042 0.151 1568 Planarity : 0.004 0.059 1812 Dihedral : 5.660 82.639 1391 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.12 % Allowed : 13.19 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.24), residues: 1273 helix: 1.91 (0.24), residues: 503 sheet: 0.70 (0.37), residues: 207 loop : -0.04 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS D 68 PHE 0.012 0.001 PHE A 633 TYR 0.017 0.001 TYR A 250 ARG 0.010 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8180 (mptt) cc_final: 0.7643 (tmtt) REVERT: A 35 MET cc_start: 0.8368 (ttp) cc_final: 0.8146 (ttp) REVERT: A 51 GLU cc_start: 0.8546 (tp30) cc_final: 0.8274 (tp30) REVERT: A 327 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8452 (mtmm) REVERT: A 465 ASP cc_start: 0.8785 (t0) cc_final: 0.8474 (m-30) REVERT: A 474 ARG cc_start: 0.7928 (ptt-90) cc_final: 0.7387 (ptt90) REVERT: A 507 THR cc_start: 0.9175 (m) cc_final: 0.8806 (p) REVERT: A 558 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 717 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8509 (t-90) REVERT: A 718 ASN cc_start: 0.8519 (t0) cc_final: 0.8029 (t0) REVERT: A 748 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8541 (pt0) REVERT: A 821 ASP cc_start: 0.8967 (t70) cc_final: 0.8712 (t0) REVERT: B 18 GLU cc_start: 0.8972 (mp0) cc_final: 0.8167 (mp0) REVERT: B 21 ASP cc_start: 0.8514 (m-30) cc_final: 0.7314 (m-30) REVERT: B 24 ASP cc_start: 0.8228 (m-30) cc_final: 0.7787 (p0) REVERT: B 64 GLU cc_start: 0.9102 (mp0) cc_final: 0.8735 (mp0) REVERT: C 34 GLN cc_start: 0.8788 (tt0) cc_final: 0.7843 (tm-30) REVERT: C 38 MET cc_start: 0.8348 (ppp) cc_final: 0.7971 (ppp) REVERT: C 66 LYS cc_start: 0.8571 (mttt) cc_final: 0.8263 (mtpt) REVERT: C 72 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8536 (mtp85) REVERT: C 92 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8213 (mm-40) REVERT: D 31 GLN cc_start: 0.8016 (tt0) cc_final: 0.7758 (tp40) REVERT: D 41 GLN cc_start: 0.8096 (mt0) cc_final: 0.7741 (mp10) outliers start: 24 outliers final: 21 residues processed: 130 average time/residue: 0.2742 time to fit residues: 48.4279 Evaluate side-chains 135 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 72 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10335 Z= 0.309 Angle : 0.556 9.371 13992 Z= 0.285 Chirality : 0.043 0.133 1568 Planarity : 0.004 0.039 1812 Dihedral : 5.521 69.918 1388 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.21 % Allowed : 13.27 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1273 helix: 1.79 (0.24), residues: 503 sheet: 0.70 (0.37), residues: 205 loop : -0.10 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 PHE 0.012 0.001 PHE A 633 TYR 0.016 0.001 TYR C 145 ARG 0.007 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8180 (mptt) cc_final: 0.7617 (tmtt) REVERT: A 35 MET cc_start: 0.8431 (ttp) cc_final: 0.8231 (ttp) REVERT: A 51 GLU cc_start: 0.8523 (tp30) cc_final: 0.8210 (tp30) REVERT: A 465 ASP cc_start: 0.8792 (t0) cc_final: 0.8471 (m-30) REVERT: A 474 ARG cc_start: 0.7976 (ptt-90) cc_final: 0.7388 (ptt90) REVERT: A 717 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8544 (t-90) REVERT: A 748 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8570 (pt0) REVERT: A 821 ASP cc_start: 0.8909 (t70) cc_final: 0.8603 (t0) REVERT: B 18 GLU cc_start: 0.8984 (mp0) cc_final: 0.8193 (mp0) REVERT: B 21 ASP cc_start: 0.8507 (m-30) cc_final: 0.7301 (m-30) REVERT: B 24 ASP cc_start: 0.8239 (m-30) cc_final: 0.7801 (p0) REVERT: B 58 ASP cc_start: 0.9085 (t0) cc_final: 0.8873 (t0) REVERT: B 64 GLU cc_start: 0.9113 (mp0) cc_final: 0.8766 (mp0) REVERT: C 34 GLN cc_start: 0.8786 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 38 MET cc_start: 0.8208 (ppp) cc_final: 0.7813 (ppp) REVERT: C 66 LYS cc_start: 0.8612 (mttt) cc_final: 0.8300 (mtpt) REVERT: C 72 ARG cc_start: 0.8938 (mmm-85) cc_final: 0.8578 (mtp85) REVERT: C 92 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8187 (mm-40) REVERT: D 31 GLN cc_start: 0.7992 (tt0) cc_final: 0.7758 (tp40) REVERT: D 41 GLN cc_start: 0.7900 (mt0) cc_final: 0.7675 (pt0) outliers start: 25 outliers final: 22 residues processed: 130 average time/residue: 0.2584 time to fit residues: 46.1187 Evaluate side-chains 138 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 0.0000 chunk 68 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 0.2980 overall best weight: 0.3142 ------------------------------------------------------------------------------- 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: 0.7887 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10335 Z= 0.149 Angle : 0.517 10.392 13992 Z= 0.260 Chirality : 0.041 0.134 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.453 78.755 1388 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.50 % Allowed : 13.98 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.26 (0.25), residues: 1273 helix: 1.91 (0.24), residues: 502 sheet: 0.72 (0.38), residues: 202 loop : -0.03 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 PHE 0.013 0.001 PHE A 633 TYR 0.016 0.001 TYR C 145 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8157 (mptt) cc_final: 0.7598 (tmtt) REVERT: A 35 MET cc_start: 0.8292 (ttp) cc_final: 0.8063 (ttm) REVERT: A 51 GLU cc_start: 0.8521 (tp30) cc_final: 0.8069 (tp30) REVERT: A 474 ARG cc_start: 0.7929 (ptt-90) cc_final: 0.7488 (ptt90) REVERT: A 507 THR cc_start: 0.9195 (m) cc_final: 0.8856 (p) REVERT: A 558 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 717 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8523 (t-90) REVERT: A 748 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8551 (pt0) REVERT: A 821 ASP cc_start: 0.8892 (t70) cc_final: 0.8570 (t0) REVERT: B 18 GLU cc_start: 0.8942 (mp0) cc_final: 0.8119 (mp0) REVERT: B 21 ASP cc_start: 0.8511 (m-30) cc_final: 0.7228 (m-30) REVERT: B 24 ASP cc_start: 0.8183 (m-30) cc_final: 0.7778 (p0) REVERT: B 58 ASP cc_start: 0.9092 (t0) cc_final: 0.8863 (t0) REVERT: B 64 GLU cc_start: 0.9080 (mp0) cc_final: 0.8727 (mp0) REVERT: C 34 GLN cc_start: 0.8775 (tt0) cc_final: 0.7854 (tm-30) REVERT: C 38 MET cc_start: 0.8209 (ppp) cc_final: 0.7813 (ppp) REVERT: C 66 LYS cc_start: 0.8586 (mttt) cc_final: 0.8288 (mtpt) REVERT: C 72 ARG cc_start: 0.8919 (mmm-85) cc_final: 0.8559 (mtp85) REVERT: C 92 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8218 (mm-40) REVERT: D 31 GLN cc_start: 0.7901 (tt0) cc_final: 0.7669 (tp40) REVERT: D 41 GLN cc_start: 0.7848 (mt0) cc_final: 0.7639 (pt0) outliers start: 17 outliers final: 14 residues processed: 130 average time/residue: 0.2790 time to fit residues: 49.3482 Evaluate side-chains 130 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10335 Z= 0.183 Angle : 0.524 9.479 13992 Z= 0.265 Chirality : 0.041 0.156 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.391 76.489 1388 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.33 % Allowed : 14.16 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.31 (0.25), residues: 1273 helix: 1.95 (0.24), residues: 502 sheet: 0.74 (0.37), residues: 202 loop : 0.01 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.004 0.001 HIS D 68 PHE 0.011 0.001 PHE A 633 TYR 0.017 0.001 TYR A 627 ARG 0.008 0.000 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8184 (mptt) cc_final: 0.7643 (tmtt) REVERT: A 35 MET cc_start: 0.8384 (ttp) cc_final: 0.8157 (ttm) REVERT: A 51 GLU cc_start: 0.8511 (tp30) cc_final: 0.8240 (tp30) REVERT: A 327 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8598 (mttp) REVERT: A 474 ARG cc_start: 0.7936 (ptt-90) cc_final: 0.7462 (ptt90) REVERT: A 507 THR cc_start: 0.9207 (m) cc_final: 0.8866 (p) REVERT: A 523 ASP cc_start: 0.8681 (t70) cc_final: 0.8449 (p0) REVERT: A 558 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 717 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8525 (t-90) REVERT: A 748 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8590 (pt0) REVERT: A 821 ASP cc_start: 0.8880 (t70) cc_final: 0.8552 (t0) REVERT: B 18 GLU cc_start: 0.8948 (mp0) cc_final: 0.8123 (mp0) REVERT: B 21 ASP cc_start: 0.8524 (m-30) cc_final: 0.7250 (m-30) REVERT: B 24 ASP cc_start: 0.8194 (m-30) cc_final: 0.7797 (p0) REVERT: B 58 ASP cc_start: 0.9103 (t0) cc_final: 0.8868 (t0) REVERT: B 64 GLU cc_start: 0.9087 (mp0) cc_final: 0.8723 (mp0) REVERT: C 34 GLN cc_start: 0.8776 (tt0) cc_final: 0.7847 (tm-30) REVERT: C 38 MET cc_start: 0.8172 (ppp) cc_final: 0.7781 (ppp) REVERT: C 66 LYS cc_start: 0.8583 (mttt) cc_final: 0.8281 (mtpt) REVERT: C 72 ARG cc_start: 0.8934 (mmm-85) cc_final: 0.8578 (mtp85) REVERT: C 92 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8201 (mm-40) REVERT: D 31 GLN cc_start: 0.7827 (tt0) cc_final: 0.7612 (tp40) outliers start: 15 outliers final: 13 residues processed: 123 average time/residue: 0.2875 time to fit residues: 48.1077 Evaluate side-chains 130 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.114751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085986 restraints weight = 20795.699| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.20 r_work: 0.3245 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10335 Z= 0.158 Angle : 0.512 10.098 13992 Z= 0.258 Chirality : 0.041 0.147 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.310 75.207 1388 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 14.07 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.34 (0.25), residues: 1273 helix: 2.00 (0.24), residues: 502 sheet: 0.63 (0.37), residues: 212 loop : 0.05 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 PHE 0.013 0.001 PHE A 633 TYR 0.015 0.001 TYR C 145 ARG 0.008 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2345.77 seconds wall clock time: 42 minutes 11.82 seconds (2531.82 seconds total)