Starting phenix.real_space_refine on Sun Dec 10 00:35:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/12_2023/7mxo_24074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/12_2023/7mxo_24074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/12_2023/7mxo_24074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/12_2023/7mxo_24074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/12_2023/7mxo_24074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/12_2023/7mxo_24074.pdb" } resolution = 3.47 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= -0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 80 5.16 5 Cl 2 4.86 5 C 8370 2.51 5 N 2111 2.21 5 O 2267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12832 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6443 Classifications: {'peptide': 825} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 795} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 6385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6385 Classifications: {'peptide': 819} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 789} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.15, per 1000 atoms: 0.56 Number of scatterers: 12832 At special positions: 0 Unit cell: (112.32, 88.56, 158.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 80 16.00 O 2267 8.00 N 2111 7.00 C 8370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 2.2 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 4 sheets defined 64.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 285 through 291 removed outlier: 4.263A pdb=" N LYS A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.785A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.752A pdb=" N VAL A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 454 removed outlier: 3.562A pdb=" N ALA A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 464 Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.552A pdb=" N GLY A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 542 Proline residue: A 519 - end of helix removed outlier: 3.876A pdb=" N LEU A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 4.331A pdb=" N SER A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 575 through 580' Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.676A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 633 removed outlier: 3.708A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 653 through 667 removed outlier: 3.801A pdb=" N LEU A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 699 Processing helix chain 'A' and resid 712 through 730 removed outlier: 3.599A pdb=" N ILE A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 751 Processing helix chain 'A' and resid 763 through 780 removed outlier: 4.303A pdb=" N TYR A 767 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 811 removed outlier: 4.000A pdb=" N LEU A 805 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 849 removed outlier: 3.539A pdb=" N GLU A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 873 Processing helix chain 'A' and resid 896 through 914 removed outlier: 3.665A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1046 Proline residue: A1040 - end of helix removed outlier: 3.687A pdb=" N LYS A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1050 Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1119 through 1130 Processing helix chain 'A' and resid 1135 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.336A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.905A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.579A pdb=" N VAL B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.271A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 500 through 506 removed outlier: 4.074A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 544 removed outlier: 3.834A pdb=" N ILE B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 519 - end of helix removed outlier: 3.586A pdb=" N LEU B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 580 removed outlier: 4.048A pdb=" N CYS B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.591A pdb=" N MET B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 633 removed outlier: 3.525A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 652 through 667 Processing helix chain 'B' and resid 674 through 699 removed outlier: 3.552A pdb=" N ILE B 678 " --> pdb=" O ILE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 731 through 752 Processing helix chain 'B' and resid 762 through 780 Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.898A pdb=" N LEU B 805 " --> pdb=" O ARG B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 849 removed outlier: 4.269A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 849 " --> pdb=" O TRP B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 873 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.840A pdb=" N VAL B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1046 Proline residue: B1040 - end of helix removed outlier: 3.962A pdb=" N LYS B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1079 Processing helix chain 'B' and resid 1090 through 1094 removed outlier: 4.402A pdb=" N ASN B1093 " --> pdb=" O GLY B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1109 removed outlier: 3.591A pdb=" N ILE B1101 " --> pdb=" O LYS B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1112 No H-bonds generated for 'chain 'B' and resid 1110 through 1112' Processing helix chain 'B' and resid 1119 through 1128 removed outlier: 3.710A pdb=" N LYS B1125 " --> pdb=" O ASP B1121 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET B1126 " --> pdb=" O ILE B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 Processing sheet with id=AA1, first strand: chain 'A' and resid 817 through 819 removed outlier: 6.398A pdb=" N GLN A 790 " --> pdb=" O THR A 883 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL A 885 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 792 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLY A 887 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N MET A 794 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 920 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET A1087 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA3, first strand: chain 'B' and resid 818 through 819 removed outlier: 6.375A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 920 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824 761 hydrogen bonds defined for protein. 2247 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: 4.04 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4003 1.34 - 1.46: 1933 1.46 - 1.57: 7039 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 13111 Sorted by residual: bond pdb=" CG1 ILE A 415 " pdb=" CD1 ILE A 415 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 bond pdb=" CG ARG B 844 " pdb=" CD ARG B 844 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CG LEU A 586 " pdb=" CD2 LEU A 586 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CB MET B 296 " pdb=" CG MET B 296 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB ILE B 603 " pdb=" CG2 ILE B 603 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.94e-01 ... (remaining 13106 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.10: 200 105.10 - 112.34: 6837 112.34 - 119.58: 4380 119.58 - 126.82: 6176 126.82 - 134.06: 179 Bond angle restraints: 17772 Sorted by residual: angle pdb=" C GLN B 843 " pdb=" N ARG B 844 " pdb=" CA ARG B 844 " ideal model delta sigma weight residual 121.14 115.43 5.71 1.75e+00 3.27e-01 1.07e+01 angle pdb=" N GLU A1106 " pdb=" CA GLU A1106 " pdb=" CB GLU A1106 " ideal model delta sigma weight residual 110.28 114.20 -3.92 1.55e+00 4.16e-01 6.38e+00 angle pdb=" CA ARG B 844 " pdb=" CB ARG B 844 " pdb=" CG ARG B 844 " ideal model delta sigma weight residual 114.10 119.13 -5.03 2.00e+00 2.50e-01 6.34e+00 angle pdb=" N MET B 835 " pdb=" CA MET B 835 " pdb=" CB MET B 835 " ideal model delta sigma weight residual 110.28 114.13 -3.85 1.55e+00 4.16e-01 6.18e+00 angle pdb=" CB MET B 835 " pdb=" CG MET B 835 " pdb=" SD MET B 835 " ideal model delta sigma weight residual 112.70 120.15 -7.45 3.00e+00 1.11e-01 6.16e+00 ... (remaining 17767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 6925 17.37 - 34.75: 711 34.75 - 52.12: 104 52.12 - 69.50: 13 69.50 - 86.87: 8 Dihedral angle restraints: 7761 sinusoidal: 3024 harmonic: 4737 Sorted by residual: dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 149.43 -56.43 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 54.48 38.52 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA PRO B 754 " pdb=" C PRO B 754 " pdb=" N ASP B 755 " pdb=" CA ASP B 755 " ideal model delta harmonic sigma weight residual 180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 7758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1357 0.034 - 0.068: 493 0.068 - 0.102: 151 0.102 - 0.136: 55 0.136 - 0.170: 3 Chirality restraints: 2059 Sorted by residual: chirality pdb=" CA ILE A 730 " pdb=" N ILE A 730 " pdb=" C ILE A 730 " pdb=" CB ILE A 730 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA ILE B 668 " pdb=" N ILE B 668 " pdb=" C ILE B 668 " pdb=" CB ILE B 668 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE A 668 " pdb=" N ILE A 668 " pdb=" C ILE A 668 " pdb=" CB ILE A 668 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2056 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 801 " 0.240 9.50e-02 1.11e+02 1.07e-01 7.15e+00 pdb=" NE ARG A 801 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 801 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 801 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 801 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1102 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ILE B1102 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE B1102 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B1103 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 495 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 496 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " 0.021 5.00e-02 4.00e+02 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 334 2.70 - 3.31: 15948 3.31 - 3.92: 24452 3.92 - 4.53: 32872 4.53 - 5.14: 50920 Nonbonded interactions: 124526 Sorted by model distance: nonbonded pdb=" OG1 THR B1094 " pdb=" NH1 ARG B1151 " model vdw 2.086 2.520 nonbonded pdb=" O GLY B 313 " pdb=" NH1 ARG B 546 " model vdw 2.088 2.520 nonbonded pdb=" O GLY A 313 " pdb=" NH1 ARG A 546 " model vdw 2.118 2.520 nonbonded pdb=" O ASP B1091 " pdb=" NH1 ARG B1151 " model vdw 2.133 2.520 nonbonded pdb=" OG1 THR B 328 " pdb=" OG1 THR B 530 " model vdw 2.144 2.440 ... (remaining 124521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 284 through 644 or resid 651 through 836 or (resid 837 and \ (name N or name CA or name C or name O or name CB )) or resid 838 through 922 o \ r resid 1020 through 1079 or resid 1081 through 1206 or resid 1301 through 1302) \ ) selection = chain 'B' } 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: 2.550 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: 0.020 Extract box with map and model: 10.130 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.840 Find NCS groups from input model: 0.790 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 0.053 13111 Z= 0.285 Angle : 0.584 7.448 17772 Z= 0.319 Chirality : 0.041 0.170 2059 Planarity : 0.004 0.107 2207 Dihedral : 13.623 86.874 4707 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.60 (0.21), residues: 1630 helix: 1.53 (0.17), residues: 973 sheet: -0.00 (0.52), residues: 110 loop : -1.65 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 287 HIS 0.004 0.001 HIS A 809 PHE 0.024 0.002 PHE A 907 TYR 0.023 0.002 TYR B 915 ARG 0.005 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2683 time to fit residues: 71.1733 Evaluate side-chains 154 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B1149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13111 Z= 0.243 Angle : 0.567 6.320 17772 Z= 0.300 Chirality : 0.043 0.153 2059 Planarity : 0.004 0.042 2207 Dihedral : 4.344 19.183 1748 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.73 % Allowed : 9.86 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.77 (0.21), residues: 1630 helix: 1.65 (0.17), residues: 976 sheet: 0.40 (0.52), residues: 97 loop : -1.59 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 892 HIS 0.002 0.001 HIS A 824 PHE 0.025 0.002 PHE A 387 TYR 0.009 0.001 TYR B 353 ARG 0.004 0.000 ARG B 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 180 average time/residue: 0.2609 time to fit residues: 68.7658 Evaluate side-chains 157 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1291 time to fit residues: 2.8420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 0.0470 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 0.0980 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 GLN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13111 Z= 0.241 Angle : 0.564 8.970 17772 Z= 0.298 Chirality : 0.042 0.173 2059 Planarity : 0.004 0.046 2207 Dihedral : 4.328 19.638 1748 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.23 % Allowed : 13.71 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.76 (0.21), residues: 1630 helix: 1.63 (0.17), residues: 978 sheet: 0.01 (0.50), residues: 114 loop : -1.54 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 892 HIS 0.003 0.001 HIS A 809 PHE 0.023 0.001 PHE B 811 TYR 0.009 0.001 TYR A1183 ARG 0.003 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 186 average time/residue: 0.2638 time to fit residues: 71.0622 Evaluate side-chains 160 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1323 time to fit residues: 3.8202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 148 optimal weight: 0.0030 chunk 157 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 42 optimal weight: 0.0000 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 ASN ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13111 Z= 0.181 Angle : 0.529 8.807 17772 Z= 0.275 Chirality : 0.040 0.154 2059 Planarity : 0.003 0.045 2207 Dihedral : 4.205 19.383 1748 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.16 % Allowed : 15.45 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.88 (0.21), residues: 1630 helix: 1.72 (0.17), residues: 987 sheet: -0.04 (0.50), residues: 112 loop : -1.52 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 892 HIS 0.005 0.001 HIS A 824 PHE 0.024 0.001 PHE B 811 TYR 0.013 0.001 TYR B 903 ARG 0.001 0.000 ARG B 828 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 179 average time/residue: 0.2607 time to fit residues: 67.2543 Evaluate side-chains 153 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1371 time to fit residues: 3.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13111 Z= 0.305 Angle : 0.599 9.727 17772 Z= 0.310 Chirality : 0.043 0.168 2059 Planarity : 0.004 0.043 2207 Dihedral : 4.350 23.118 1748 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.23 % Allowed : 17.62 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.66 (0.21), residues: 1630 helix: 1.50 (0.16), residues: 990 sheet: -0.01 (0.49), residues: 114 loop : -1.55 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 892 HIS 0.005 0.001 HIS A 398 PHE 0.023 0.002 PHE B 811 TYR 0.009 0.001 TYR B 767 ARG 0.002 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.472 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 outliers start: 17 outliers final: 10 residues processed: 167 average time/residue: 0.2548 time to fit residues: 63.0174 Evaluate side-chains 160 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1311 time to fit residues: 4.3782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13111 Z= 0.216 Angle : 0.554 9.457 17772 Z= 0.287 Chirality : 0.041 0.165 2059 Planarity : 0.003 0.043 2207 Dihedral : 4.293 34.995 1748 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.65 % Allowed : 18.78 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.75 (0.21), residues: 1630 helix: 1.59 (0.17), residues: 992 sheet: 0.09 (0.49), residues: 114 loop : -1.58 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 892 HIS 0.005 0.001 HIS A 824 PHE 0.023 0.001 PHE B 811 TYR 0.013 0.001 TYR A 739 ARG 0.003 0.000 ARG B 844 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 170 average time/residue: 0.2640 time to fit residues: 65.1344 Evaluate side-chains 155 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1281 time to fit residues: 3.2988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 157 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 72 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13111 Z= 0.205 Angle : 0.558 11.162 17772 Z= 0.288 Chirality : 0.041 0.172 2059 Planarity : 0.003 0.042 2207 Dihedral : 4.243 37.565 1748 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.73 % Allowed : 19.07 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.78 (0.21), residues: 1630 helix: 1.61 (0.17), residues: 1000 sheet: 0.09 (0.49), residues: 115 loop : -1.58 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 892 HIS 0.003 0.001 HIS A 824 PHE 0.023 0.001 PHE B 811 TYR 0.011 0.001 TYR A 739 ARG 0.001 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 169 average time/residue: 0.2863 time to fit residues: 70.4177 Evaluate side-chains 161 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1240 time to fit residues: 3.5476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.0050 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 99 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13111 Z= 0.175 Angle : 0.547 10.958 17772 Z= 0.281 Chirality : 0.040 0.181 2059 Planarity : 0.003 0.043 2207 Dihedral : 4.204 38.244 1748 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.51 % Allowed : 19.51 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.87 (0.21), residues: 1630 helix: 1.72 (0.17), residues: 994 sheet: 0.13 (0.49), residues: 115 loop : -1.61 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 892 HIS 0.003 0.000 HIS A 824 PHE 0.024 0.001 PHE B 811 TYR 0.012 0.001 TYR B 903 ARG 0.001 0.000 ARG B 828 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 165 average time/residue: 0.2864 time to fit residues: 68.4870 Evaluate side-chains 159 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1313 time to fit residues: 2.9193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 138 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13111 Z= 0.237 Angle : 0.584 11.559 17772 Z= 0.300 Chirality : 0.042 0.199 2059 Planarity : 0.003 0.042 2207 Dihedral : 4.269 39.254 1748 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.44 % Allowed : 20.09 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.79 (0.21), residues: 1630 helix: 1.63 (0.17), residues: 995 sheet: 0.14 (0.50), residues: 115 loop : -1.61 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 892 HIS 0.003 0.001 HIS A 824 PHE 0.025 0.001 PHE B 811 TYR 0.013 0.001 TYR A 739 ARG 0.005 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 163 average time/residue: 0.2748 time to fit residues: 64.6448 Evaluate side-chains 159 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1308 time to fit residues: 2.7516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 149 optimal weight: 0.0060 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13111 Z= 0.167 Angle : 0.557 11.670 17772 Z= 0.285 Chirality : 0.040 0.214 2059 Planarity : 0.003 0.042 2207 Dihedral : 4.166 40.982 1748 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.29 % Allowed : 19.72 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.88 (0.21), residues: 1630 helix: 1.73 (0.17), residues: 1000 sheet: 0.15 (0.50), residues: 113 loop : -1.66 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 892 HIS 0.004 0.001 HIS A 824 PHE 0.024 0.001 PHE B 811 TYR 0.018 0.001 TYR B 915 ARG 0.006 0.000 ARG A 801 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.391 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 outliers start: 4 outliers final: 3 residues processed: 162 average time/residue: 0.2764 time to fit residues: 64.4621 Evaluate side-chains 153 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1401 time to fit residues: 2.6900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 0.0020 chunk 54 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.203291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134365 restraints weight = 16306.252| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.07 r_work: 0.3351 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13111 Z= 0.189 Angle : 0.578 12.484 17772 Z= 0.298 Chirality : 0.041 0.208 2059 Planarity : 0.003 0.042 2207 Dihedral : 4.154 40.067 1748 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.07 % Allowed : 20.45 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.82 (0.21), residues: 1630 helix: 1.69 (0.17), residues: 998 sheet: 0.24 (0.50), residues: 115 loop : -1.73 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 892 HIS 0.002 0.000 HIS A 824 PHE 0.025 0.001 PHE B 811 TYR 0.008 0.001 TYR A 353 ARG 0.006 0.000 ARG A 801 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.36 seconds wall clock time: 51 minutes 10.46 seconds (3070.46 seconds total)