Starting phenix.real_space_refine on Wed May 15 21:36:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s3e_19691/05_2024/8s3e_19691_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s3e_19691/05_2024/8s3e_19691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s3e_19691/05_2024/8s3e_19691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s3e_19691/05_2024/8s3e_19691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s3e_19691/05_2024/8s3e_19691_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s3e_19691/05_2024/8s3e_19691_updated.pdb" } resolution = 2.39 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= 1.000 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 24 5.49 5 Mg 4 5.21 5 S 208 5.16 5 C 20632 2.51 5 N 5012 2.21 5 O 5693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 601": "OD1" <-> "OD2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A ASP 931": "OD1" <-> "OD2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1040": "OE1" <-> "OE2" Residue "B PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 601": "OD1" <-> "OD2" Residue "B GLU 750": "OE1" <-> "OE2" Residue "B ASP 931": "OD1" <-> "OD2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1040": "OE1" <-> "OE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 601": "OD1" <-> "OD2" Residue "C GLU 750": "OE1" <-> "OE2" Residue "C ASP 931": "OD1" <-> "OD2" Residue "C GLU 948": "OE1" <-> "OE2" Residue "C PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1040": "OE1" <-> "OE2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 601": "OD1" <-> "OD2" Residue "D GLU 750": "OE1" <-> "OE2" Residue "D ASP 931": "OD1" <-> "OD2" Residue "D GLU 948": "OE1" <-> "OE2" Residue "D PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1040": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 31585 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "B" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "C" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "D" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "E" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "F" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "G" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "H" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "A" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 335 Unusual residues: {' K': 2, ' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Unusual residues: {' K': 1, ' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Unusual residues: {' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Unusual residues: {' K': 1, ' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 15.42, per 1000 atoms: 0.49 Number of scatterers: 31585 At special positions: 0 Unit cell: (142.12, 142.12, 129.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 208 16.00 P 24 15.00 Mg 4 11.99 O 5693 8.00 N 5012 7.00 C 20632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.36 Conformation dependent library (CDL) restraints added in 5.4 seconds 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 24 sheets defined 50.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.85 Creating SS restraints... Processing helix chain 'A' and resid 22 through 53 removed outlier: 3.766A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 105 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.302A pdb=" N SER A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 181 through 199 Proline residue: A 191 - end of helix removed outlier: 3.987A pdb=" N TYR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 223 removed outlier: 4.085A pdb=" N SER A 218 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 298 through 327 removed outlier: 3.819A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.786A pdb=" N HIS A 468 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.503A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.836A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 703 No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 735 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 760 through 769 removed outlier: 4.926A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 792 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 818 through 828 Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.540A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 917 through 929 removed outlier: 3.749A pdb=" N SER A 922 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 924 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 925 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 929 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 947 through 956 Processing helix chain 'A' and resid 966 through 969 removed outlier: 3.687A pdb=" N LEU A 969 " --> pdb=" O PRO A 966 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 966 through 969' Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.474A pdb=" N ASP A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 990 " --> pdb=" O PHE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'B' and resid 22 through 53 removed outlier: 3.766A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 Processing helix chain 'B' and resid 110 through 135 removed outlier: 4.302A pdb=" N SER B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 170 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 181 through 199 Proline residue: B 191 - end of helix removed outlier: 3.986A pdb=" N TYR B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 223 removed outlier: 4.086A pdb=" N SER B 218 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 298 through 327 removed outlier: 3.819A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 433 through 450 Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.786A pdb=" N HIS B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 Processing helix chain 'B' and resid 503 through 511 removed outlier: 3.503A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.836A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'B' and resid 735 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'B' and resid 760 through 769 removed outlier: 4.925A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 792 Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 818 through 828 Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.541A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 910 No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 917 through 929 removed outlier: 3.750A pdb=" N SER B 922 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 925 " --> pdb=" O SER B 922 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 929 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 947 through 956 Processing helix chain 'B' and resid 966 through 969 removed outlier: 3.686A pdb=" N LEU B 969 " --> pdb=" O PRO B 966 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 966 through 969' Processing helix chain 'B' and resid 985 through 991 removed outlier: 4.475A pdb=" N ASP B 989 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 990 " --> pdb=" O PHE B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'C' and resid 22 through 53 removed outlier: 3.766A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 110 through 135 removed outlier: 4.302A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 170 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 181 through 199 Proline residue: C 191 - end of helix removed outlier: 3.986A pdb=" N TYR C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 223 removed outlier: 4.086A pdb=" N SER C 218 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 259 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 298 through 327 removed outlier: 3.819A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 433 through 450 Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.786A pdb=" N HIS C 468 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 499 Processing helix chain 'C' and resid 503 through 511 removed outlier: 3.504A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 602 through 609 removed outlier: 3.837A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 703 No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 735 through 742 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 748 through 750 No H-bonds generated for 'chain 'C' and resid 748 through 750' Processing helix chain 'C' and resid 760 through 769 removed outlier: 4.925A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 792 Processing helix chain 'C' and resid 794 through 796 No H-bonds generated for 'chain 'C' and resid 794 through 796' Processing helix chain 'C' and resid 805 through 807 No H-bonds generated for 'chain 'C' and resid 805 through 807' Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing helix chain 'C' and resid 818 through 828 Processing helix chain 'C' and resid 873 through 875 No H-bonds generated for 'chain 'C' and resid 873 through 875' Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.540A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 917 through 929 removed outlier: 3.750A pdb=" N SER C 922 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET C 924 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 925 " --> pdb=" O SER C 922 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 929 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 947 through 956 Processing helix chain 'C' and resid 966 through 969 removed outlier: 3.687A pdb=" N LEU C 969 " --> pdb=" O PRO C 966 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 966 through 969' Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.475A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 990 " --> pdb=" O PHE C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.766A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 110 through 135 removed outlier: 4.303A pdb=" N SER D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 181 through 199 Proline residue: D 191 - end of helix removed outlier: 3.986A pdb=" N TYR D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 223 removed outlier: 4.086A pdb=" N SER D 218 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 259 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 298 through 327 removed outlier: 3.819A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 433 through 450 Processing helix chain 'D' and resid 463 through 471 removed outlier: 3.786A pdb=" N HIS D 468 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 499 Processing helix chain 'D' and resid 503 through 511 removed outlier: 3.503A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 602 through 609 removed outlier: 3.835A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 609 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 703 No H-bonds generated for 'chain 'D' and resid 700 through 703' Processing helix chain 'D' and resid 707 through 712 Processing helix chain 'D' and resid 735 through 742 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 748 through 750 No H-bonds generated for 'chain 'D' and resid 748 through 750' Processing helix chain 'D' and resid 760 through 769 removed outlier: 4.925A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 792 Processing helix chain 'D' and resid 794 through 796 No H-bonds generated for 'chain 'D' and resid 794 through 796' Processing helix chain 'D' and resid 805 through 807 No H-bonds generated for 'chain 'D' and resid 805 through 807' Processing helix chain 'D' and resid 813 through 815 No H-bonds generated for 'chain 'D' and resid 813 through 815' Processing helix chain 'D' and resid 818 through 828 Processing helix chain 'D' and resid 873 through 875 No H-bonds generated for 'chain 'D' and resid 873 through 875' Processing helix chain 'D' and resid 885 through 890 removed outlier: 3.540A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 910 No H-bonds generated for 'chain 'D' and resid 907 through 910' Processing helix chain 'D' and resid 917 through 929 removed outlier: 3.749A pdb=" N SER D 922 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET D 924 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER D 925 " --> pdb=" O SER D 922 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE D 929 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 933 through 941 Processing helix chain 'D' and resid 947 through 956 Processing helix chain 'D' and resid 966 through 969 removed outlier: 3.687A pdb=" N LEU D 969 " --> pdb=" O PRO D 966 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 966 through 969' Processing helix chain 'D' and resid 985 through 991 removed outlier: 4.475A pdb=" N ASP D 989 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 990 " --> pdb=" O PHE D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1007 Processing helix chain 'E' and resid 259 through 296 removed outlier: 5.270A pdb=" N GLY E 269 " --> pdb=" O ILE E 265 " (cutoff:3.500A) Proline residue: E 270 - end of helix Processing helix chain 'F' and resid 259 through 296 removed outlier: 5.270A pdb=" N GLY F 269 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Proline residue: F 270 - end of helix Processing helix chain 'G' and resid 259 through 296 removed outlier: 5.270A pdb=" N GLY G 269 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Proline residue: G 270 - end of helix Processing helix chain 'H' and resid 259 through 296 removed outlier: 5.269A pdb=" N GLY H 269 " --> pdb=" O ILE H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 139 through 141 Processing sheet with id= B, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.615A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.043A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 878 through 880 removed outlier: 6.724A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS A 753 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL A 721 " --> pdb=" O HIS A 753 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 755 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 723 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL A 757 " --> pdb=" O ILE A 723 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 976 through 981 Processing sheet with id= F, first strand: chain 'A' and resid 1013 through 1017 Processing sheet with id= G, first strand: chain 'B' and resid 139 through 141 Processing sheet with id= H, first strand: chain 'B' and resid 482 through 485 removed outlier: 6.615A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.042A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 878 through 880 removed outlier: 6.725A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS B 753 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL B 721 " --> pdb=" O HIS B 753 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 755 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE B 723 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL B 757 " --> pdb=" O ILE B 723 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 976 through 981 Processing sheet with id= L, first strand: chain 'B' and resid 1013 through 1017 Processing sheet with id= M, first strand: chain 'C' and resid 139 through 141 Processing sheet with id= N, first strand: chain 'C' and resid 482 through 485 removed outlier: 6.614A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.043A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 878 through 880 removed outlier: 6.724A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS C 753 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL C 721 " --> pdb=" O HIS C 753 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 755 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 723 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL C 757 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 976 through 981 Processing sheet with id= R, first strand: chain 'C' and resid 1013 through 1017 Processing sheet with id= S, first strand: chain 'D' and resid 139 through 141 Processing sheet with id= T, first strand: chain 'D' and resid 482 through 485 removed outlier: 6.615A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.042A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 878 through 880 removed outlier: 6.724A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N HIS D 753 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL D 721 " --> pdb=" O HIS D 753 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL D 755 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE D 723 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL D 757 " --> pdb=" O ILE D 723 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 976 through 981 Processing sheet with id= X, first strand: chain 'D' and resid 1013 through 1017 1320 hydrogen bonds defined for protein. 3636 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: 12.08 Time building geometry restraints manager: 13.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5438 1.33 - 1.45: 8260 1.45 - 1.57: 18202 1.57 - 1.69: 48 1.69 - 1.81: 304 Bond restraints: 32252 Sorted by residual: bond pdb=" O1P 6PL C1202 " pdb=" P 6PL C1202 " ideal model delta sigma weight residual 1.502 1.652 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" O1P 6PL B1202 " pdb=" P 6PL B1202 " ideal model delta sigma weight residual 1.502 1.651 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" O4P 6PL C1202 " pdb=" P 6PL C1202 " ideal model delta sigma weight residual 1.651 1.502 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O1P 6PL A1216 " pdb=" P 6PL A1216 " ideal model delta sigma weight residual 1.502 1.651 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O4P 6PL B1202 " pdb=" P 6PL B1202 " ideal model delta sigma weight residual 1.651 1.502 0.149 2.00e-02 2.50e+03 5.54e+01 ... (remaining 32247 not shown) Histogram of bond angle deviations from ideal: 80.66 - 91.33: 12 91.33 - 102.00: 132 102.00 - 112.67: 17667 112.67 - 123.34: 24866 123.34 - 134.01: 1039 Bond angle restraints: 43716 Sorted by residual: angle pdb=" C12 CLR C1206 " pdb=" C13 CLR C1206 " pdb=" C18 CLR C1206 " ideal model delta sigma weight residual 111.01 81.09 29.92 3.00e+00 1.11e-01 9.94e+01 angle pdb=" C12 CLR B1206 " pdb=" C13 CLR B1206 " pdb=" C18 CLR B1206 " ideal model delta sigma weight residual 111.01 81.13 29.88 3.00e+00 1.11e-01 9.92e+01 angle pdb=" C12 CLR A1204 " pdb=" C13 CLR A1204 " pdb=" C18 CLR A1204 " ideal model delta sigma weight residual 111.01 81.14 29.87 3.00e+00 1.11e-01 9.91e+01 angle pdb=" C12 CLR D1206 " pdb=" C13 CLR D1206 " pdb=" C18 CLR D1206 " ideal model delta sigma weight residual 111.01 81.16 29.85 3.00e+00 1.11e-01 9.90e+01 angle pdb=" C17 CLR B1206 " pdb=" C13 CLR B1206 " pdb=" C18 CLR B1206 " ideal model delta sigma weight residual 110.18 80.66 29.52 3.00e+00 1.11e-01 9.68e+01 ... (remaining 43711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 19404 35.11 - 70.21: 580 70.21 - 105.32: 4 105.32 - 140.42: 0 140.42 - 175.53: 20 Dihedral angle restraints: 20008 sinusoidal: 8896 harmonic: 11112 Sorted by residual: dihedral pdb=" C18 CLR C1206 " pdb=" C13 CLR C1206 " pdb=" C17 CLR C1206 " pdb=" C20 CLR C1206 " ideal model delta sinusoidal sigma weight residual 312.73 137.20 175.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 CLR D1206 " pdb=" C13 CLR D1206 " pdb=" C17 CLR D1206 " pdb=" C20 CLR D1206 " ideal model delta sinusoidal sigma weight residual 312.73 137.23 175.50 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 CLR A1204 " pdb=" C13 CLR A1204 " pdb=" C17 CLR A1204 " pdb=" C20 CLR A1204 " ideal model delta sinusoidal sigma weight residual 312.73 137.24 175.49 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 20005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.377: 4968 0.377 - 0.753: 0 0.753 - 1.130: 0 1.130 - 1.507: 0 1.507 - 1.883: 4 Chirality restraints: 4972 Sorted by residual: chirality pdb=" C13 CLR A1204 " pdb=" C12 CLR A1204 " pdb=" C14 CLR A1204 " pdb=" C17 CLR A1204 " both_signs ideal model delta sigma weight residual False -2.93 -1.05 -1.88 2.00e-01 2.50e+01 8.87e+01 chirality pdb=" C13 CLR D1206 " pdb=" C12 CLR D1206 " pdb=" C14 CLR D1206 " pdb=" C17 CLR D1206 " both_signs ideal model delta sigma weight residual False -2.93 -1.05 -1.88 2.00e-01 2.50e+01 8.86e+01 chirality pdb=" C13 CLR C1206 " pdb=" C12 CLR C1206 " pdb=" C14 CLR C1206 " pdb=" C17 CLR C1206 " both_signs ideal model delta sigma weight residual False -2.93 -1.05 -1.88 2.00e-01 2.50e+01 8.82e+01 ... (remaining 4969 not shown) Planarity restraints: 5324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 191 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 192 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 192 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 191 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO D 192 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " -0.026 5.00e-02 4.00e+02 ... (remaining 5321 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.71: 910 2.71 - 3.32: 36650 3.32 - 3.93: 62002 3.93 - 4.53: 85288 4.53 - 5.14: 128693 Nonbonded interactions: 313543 Sorted by model distance: nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR B 290 " model vdw 2.107 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.221 2.440 nonbonded pdb=" O ARG G 295 " pdb=" NE2 GLN G 298 " model vdw 2.238 2.520 nonbonded pdb=" O ARG F 295 " pdb=" NE2 GLN F 298 " model vdw 2.238 2.520 ... (remaining 313538 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 19 through 1060 or resid 1203 through 1204 or (resid 1209 \ and (name N or name C1 or name C11 or name C12 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or nam \ e O4P or name P )) or (resid 1210 and (name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name O11 or name O2 or name O3 or name O31)) or (resid 1 \ 211 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name O11 or name O2 or name O3 or name O3P)) or (resid 1212 and (nam \ e C1 or name C11 or name C12 or name C2 or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name O3 or name O31 or name O3P)) or (resid 1213 and (name C1 or name C11 or n \ ame C12 or name O11 or name O2 or name O3 or name O3P)) or resid 1214 or (resid \ 1216 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C2 or name C3 or name O11 or name O1P or name O2 o \ r name O2P or name O3 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 19 through 1060 or resid 1203 through 1204 or resid 1209 o \ r (resid 1210 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name O11 or name O2 or name O3 or name O31)) or (resid 1211 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O11 \ or name O2 or name O3 or name O3P)) or (resid 1212 and (name C1 or name C11 or \ name C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name O3 or name O3 \ 1 or name O3P)) or (resid 1213 and (name C1 or name C11 or name C12 or name O11 \ or name O2 or name O3 or name O3P)) or resid 1214 or (resid 1216 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C2 or name C3 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 19 through 1060 or resid 1203 through 1204 or resid 1209 o \ r (resid 1210 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name O11 or name O2 or name O3 or name O31)) or (resid 1211 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O11 \ or name O2 or name O3 or name O3P)) or (resid 1212 and (name C1 or name C11 or \ name C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name O3 or name O3 \ 1 or name O3P)) or (resid 1213 and (name C1 or name C11 or name C12 or name O11 \ or name O2 or name O3 or name O3P)) or resid 1214 or (resid 1216 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C2 or name C3 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 19 through 1060 or resid 1203 through 1204 or resid 1209 o \ r (resid 1210 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name O11 or name O2 or name O3 or name O31)) or (resid 1211 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O11 \ or name O2 or name O3 or name O3P)) or (resid 1212 and (name C1 or name C11 or \ name C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name O3 or name O3 \ 1 or name O3P)) or (resid 1213 and (name C1 or name C11 or name C12 or name O11 \ or name O2 or name O3 or name O3P)) or resid 1214 or (resid 1216 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C2 or name C3 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O3P or name O4P or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 8.190 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: 0.030 Extract box with map and model: 28.980 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 82.580 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 32252 Z= 0.230 Angle : 0.764 29.916 43716 Z= 0.332 Chirality : 0.066 1.883 4972 Planarity : 0.003 0.046 5324 Dihedral : 16.608 175.530 12808 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.81 % Allowed : 14.63 % Favored : 83.56 % 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: 0.94 (0.14), residues: 3752 helix: 1.08 (0.12), residues: 1900 sheet: 0.44 (0.28), residues: 356 loop : 0.26 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.004 0.001 HIS C 586 PHE 0.025 0.001 PHE D 550 TYR 0.013 0.001 TYR B1032 ARG 0.005 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 385 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 555 GLU cc_start: 0.6433 (mt-10) cc_final: 0.6074 (mt-10) REVERT: B 960 ARG cc_start: 0.4490 (pmt-80) cc_final: 0.4209 (ppt170) REVERT: G 287 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (mt) outliers start: 60 outliers final: 35 residues processed: 426 average time/residue: 1.1964 time to fit residues: 621.5634 Evaluate side-chains 378 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 342 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 816 GLN Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 816 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 288 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.7980 chunk 284 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 0.4980 chunk 152 optimal weight: 0.8980 chunk 294 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 341 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 747 HIS A 771 HIS B 142 GLN B 222 GLN B 771 HIS C 142 GLN C 222 GLN C 397 GLN C 747 HIS C 771 HIS D 142 GLN D 222 GLN D 397 GLN D 771 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32252 Z= 0.141 Angle : 0.674 30.806 43716 Z= 0.283 Chirality : 0.063 1.764 4972 Planarity : 0.003 0.047 5324 Dihedral : 13.799 179.132 5900 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.56 % Allowed : 13.30 % Favored : 83.14 % 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: 1.15 (0.14), residues: 3752 helix: 1.29 (0.12), residues: 1900 sheet: 0.41 (0.29), residues: 348 loop : 0.34 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 93 HIS 0.003 0.001 HIS D 586 PHE 0.016 0.001 PHE D 144 TYR 0.016 0.001 TYR C 762 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 377 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 794 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8045 (tp) REVERT: A 953 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7711 (mp) REVERT: B 794 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7854 (tp) REVERT: B 960 ARG cc_start: 0.4472 (pmt-80) cc_final: 0.4241 (ppt170) REVERT: C 794 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8048 (tp) REVERT: D 281 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8497 (mp) REVERT: D 518 LYS cc_start: 0.5539 (mmtm) cc_final: 0.5337 (mmtm) REVERT: E 264 MET cc_start: 0.7483 (ptm) cc_final: 0.7213 (ptt) REVERT: F 264 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7195 (ptt) outliers start: 118 outliers final: 36 residues processed: 450 average time/residue: 1.1549 time to fit residues: 641.4819 Evaluate side-chains 387 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 344 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 342 optimal weight: 3.9990 chunk 369 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 339 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 747 HIS A 771 HIS B 142 GLN B 771 HIS C 142 GLN C 771 HIS D 142 GLN D 468 HIS D 771 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32252 Z= 0.180 Angle : 0.691 31.018 43716 Z= 0.293 Chirality : 0.063 1.755 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.539 177.658 5859 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.98 % Allowed : 13.69 % Favored : 82.33 % 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: 1.16 (0.14), residues: 3752 helix: 1.31 (0.12), residues: 1896 sheet: 0.32 (0.28), residues: 348 loop : 0.34 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 43 HIS 0.003 0.001 HIS B 586 PHE 0.020 0.001 PHE D 144 TYR 0.017 0.002 TYR B1007 ARG 0.003 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 389 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8613 (mp) REVERT: A 794 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 953 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7726 (mp) REVERT: B 281 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8569 (mp) REVERT: B 555 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6149 (mp0) REVERT: B 556 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.8006 (mm) REVERT: B 560 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7322 (mppt) REVERT: B 794 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7872 (tp) REVERT: C 442 MET cc_start: 0.6553 (mmt) cc_final: 0.6346 (mmt) REVERT: C 685 LYS cc_start: 0.5358 (OUTLIER) cc_final: 0.5089 (ptpt) REVERT: C 794 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8080 (tp) REVERT: D 281 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8616 (mp) REVERT: D 555 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6308 (mt-10) REVERT: D 794 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7896 (tp) REVERT: E 264 MET cc_start: 0.7542 (ptm) cc_final: 0.7297 (ptt) REVERT: F 264 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7326 (ptt) outliers start: 132 outliers final: 51 residues processed: 459 average time/residue: 1.2411 time to fit residues: 699.0455 Evaluate side-chains 421 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 359 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 276 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 343 optimal weight: 0.9990 chunk 363 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 325 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 771 HIS B 142 GLN B 468 HIS B 747 HIS C 142 GLN C 200 ASN C 468 HIS C 747 HIS C 771 HIS D 142 GLN D 468 HIS D 747 HIS D 771 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32252 Z= 0.259 Angle : 0.734 31.348 43716 Z= 0.319 Chirality : 0.065 1.744 4972 Planarity : 0.004 0.052 5324 Dihedral : 13.558 175.684 5851 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.10 % Allowed : 14.17 % Favored : 81.72 % 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: 0.93 (0.14), residues: 3752 helix: 1.13 (0.12), residues: 1896 sheet: 0.26 (0.27), residues: 368 loop : 0.21 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.005 0.001 HIS C 718 PHE 0.020 0.002 PHE D1012 TYR 0.020 0.002 TYR D 198 ARG 0.004 0.000 ARG B 974 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 400 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6029 (tp) REVERT: A 764 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7921 (pttp) REVERT: A 794 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 953 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 604 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6885 (mt-10) REVERT: B 794 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7942 (tp) REVERT: C 506 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6282 (tpt) REVERT: D 43 TRP cc_start: 0.5758 (t-100) cc_final: 0.5366 (t-100) REVERT: D 764 LYS cc_start: 0.8327 (ptpp) cc_final: 0.7911 (pttp) REVERT: D 794 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7961 (tp) REVERT: E 264 MET cc_start: 0.7645 (ptm) cc_final: 0.7430 (ptt) REVERT: F 264 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7465 (ptt) outliers start: 136 outliers final: 74 residues processed: 473 average time/residue: 1.1861 time to fit residues: 688.8554 Evaluate side-chains 453 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 371 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 1035 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 759 SER Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 1035 THR Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 0.1980 chunk 206 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 270 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 326 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 771 HIS B 142 GLN C 142 GLN C 200 ASN C 771 HIS D 142 GLN D 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32252 Z= 0.149 Angle : 0.689 30.916 43716 Z= 0.292 Chirality : 0.063 1.750 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.388 175.981 5851 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.32 % Allowed : 15.74 % Favored : 80.94 % 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: 1.10 (0.14), residues: 3752 helix: 1.29 (0.12), residues: 1896 sheet: 0.24 (0.28), residues: 348 loop : 0.29 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 477 HIS 0.003 0.001 HIS A 586 PHE 0.020 0.001 PHE D 550 TYR 0.012 0.001 TYR D 762 ARG 0.002 0.000 ARG F 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 400 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 953 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7785 (mp) REVERT: C 281 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 506 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6196 (tpt) REVERT: D 43 TRP cc_start: 0.5766 (t-100) cc_final: 0.5380 (t-100) REVERT: D 329 ARG cc_start: 0.7282 (ppt90) cc_final: 0.6776 (ptt90) REVERT: D 794 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7924 (tp) REVERT: D 952 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7866 (mt) outliers start: 110 outliers final: 49 residues processed: 458 average time/residue: 1.1866 time to fit residues: 666.9108 Evaluate side-chains 427 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 373 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 0.8980 chunk 327 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 213 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 363 optimal weight: 5.9990 chunk 301 optimal weight: 0.0770 chunk 168 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS A 771 HIS ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN C 771 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32252 Z= 0.151 Angle : 0.691 30.974 43716 Z= 0.291 Chirality : 0.063 1.747 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.257 175.924 5847 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.41 % Allowed : 15.89 % Favored : 80.70 % 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: 1.12 (0.14), residues: 3752 helix: 1.33 (0.12), residues: 1896 sheet: 0.20 (0.28), residues: 348 loop : 0.29 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.003 0.001 HIS D 468 PHE 0.022 0.001 PHE B 550 TYR 0.019 0.001 TYR A1032 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 399 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 794 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (tp) REVERT: A 953 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7762 (mp) REVERT: B 794 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7923 (tp) REVERT: C 281 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 794 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8026 (tp) REVERT: D 43 TRP cc_start: 0.5793 (t-100) cc_final: 0.5380 (t-100) REVERT: D 281 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 794 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7916 (tp) REVERT: D 952 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7584 (mt) outliers start: 113 outliers final: 51 residues processed: 464 average time/residue: 1.1905 time to fit residues: 680.0235 Evaluate side-chains 432 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 372 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 8.9990 chunk 41 optimal weight: 0.4980 chunk 207 optimal weight: 0.5980 chunk 265 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 306 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 362 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 167 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 142 GLN C 142 GLN C 771 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS D 753 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32252 Z= 0.145 Angle : 0.689 30.956 43716 Z= 0.291 Chirality : 0.063 1.747 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.132 176.010 5847 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.23 % Allowed : 16.22 % Favored : 80.55 % 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: 1.16 (0.14), residues: 3752 helix: 1.39 (0.12), residues: 1892 sheet: 0.14 (0.28), residues: 348 loop : 0.28 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 477 HIS 0.003 0.001 HIS A 586 PHE 0.018 0.001 PHE C 34 TYR 0.017 0.001 TYR A1032 ARG 0.004 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 384 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.6415 (mmt) cc_final: 0.6208 (mmt) REVERT: A 447 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6043 (tp) REVERT: A 953 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 604 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: B 794 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7925 (tp) REVERT: D 43 TRP cc_start: 0.5809 (t-100) cc_final: 0.5399 (t-100) REVERT: D 794 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7928 (tp) REVERT: D 952 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (mt) REVERT: E 264 MET cc_start: 0.7562 (ptm) cc_final: 0.7347 (ptt) outliers start: 107 outliers final: 52 residues processed: 447 average time/residue: 1.1424 time to fit residues: 629.3742 Evaluate side-chains 428 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 370 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 179 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 771 HIS B 142 GLN C 142 GLN C 771 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32252 Z= 0.167 Angle : 0.704 31.055 43716 Z= 0.299 Chirality : 0.063 1.745 4972 Planarity : 0.003 0.050 5324 Dihedral : 13.085 175.748 5844 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.83 % Allowed : 17.10 % Favored : 80.07 % 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: 1.11 (0.14), residues: 3752 helix: 1.33 (0.12), residues: 1896 sheet: 0.08 (0.28), residues: 348 loop : 0.29 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 477 HIS 0.003 0.001 HIS D 753 PHE 0.027 0.001 PHE B 550 TYR 0.018 0.001 TYR A1032 ARG 0.007 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 386 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8012 (tp) REVERT: A 953 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 604 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: B 794 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7938 (tp) REVERT: C 794 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8005 (tp) REVERT: D 43 TRP cc_start: 0.5878 (t-100) cc_final: 0.5463 (t-100) REVERT: D 794 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7948 (tp) REVERT: D 953 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7767 (mp) REVERT: E 264 MET cc_start: 0.7605 (ptm) cc_final: 0.7383 (ptt) outliers start: 94 outliers final: 58 residues processed: 444 average time/residue: 1.1683 time to fit residues: 637.0834 Evaluate side-chains 441 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 376 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 276 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 337 optimal weight: 0.8980 chunk 203 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 305 optimal weight: 0.0570 chunk 319 optimal weight: 0.9990 chunk 336 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS B 142 GLN C 142 GLN C 771 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32252 Z= 0.163 Angle : 0.704 31.023 43716 Z= 0.299 Chirality : 0.063 1.745 4972 Planarity : 0.003 0.050 5324 Dihedral : 13.038 175.715 5844 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.59 % Allowed : 17.46 % Favored : 79.95 % 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: 1.10 (0.14), residues: 3752 helix: 1.32 (0.12), residues: 1896 sheet: 0.09 (0.28), residues: 348 loop : 0.29 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 477 HIS 0.003 0.001 HIS D 753 PHE 0.019 0.001 PHE C 34 TYR 0.018 0.001 TYR A1032 ARG 0.005 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 385 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8027 (tp) REVERT: A 953 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7796 (mp) REVERT: B 604 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: B 794 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7937 (tp) REVERT: B 1018 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6347 (ttp-170) REVERT: C 794 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (tp) REVERT: D 43 TRP cc_start: 0.5902 (t-100) cc_final: 0.5500 (t-100) REVERT: D 794 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7955 (tp) REVERT: D 953 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (mp) REVERT: F 264 MET cc_start: 0.7567 (ptm) cc_final: 0.7328 (ptt) outliers start: 86 outliers final: 61 residues processed: 440 average time/residue: 1.1546 time to fit residues: 624.5489 Evaluate side-chains 439 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 370 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 248 optimal weight: 0.7980 chunk 374 optimal weight: 4.9990 chunk 344 optimal weight: 0.5980 chunk 298 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 771 HIS B 142 GLN C 142 GLN C 200 ASN C 771 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32252 Z= 0.156 Angle : 0.707 31.005 43716 Z= 0.300 Chirality : 0.064 1.745 4972 Planarity : 0.003 0.048 5324 Dihedral : 12.992 175.802 5844 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.29 % Allowed : 17.85 % Favored : 79.86 % 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: 1.10 (0.14), residues: 3752 helix: 1.32 (0.12), residues: 1896 sheet: 0.08 (0.28), residues: 348 loop : 0.29 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 694 HIS 0.003 0.001 HIS D 753 PHE 0.021 0.001 PHE C 34 TYR 0.025 0.001 TYR D1007 ARG 0.006 0.000 ARG C 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 384 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 953 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7789 (mp) REVERT: B 604 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: B 794 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7945 (tp) REVERT: C 43 TRP cc_start: 0.5799 (t-100) cc_final: 0.5480 (t-100) REVERT: C 794 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8036 (tp) REVERT: D 43 TRP cc_start: 0.5930 (t-100) cc_final: 0.5525 (t-100) REVERT: D 506 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6141 (tpt) REVERT: D 794 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (tp) REVERT: F 264 MET cc_start: 0.7604 (ptm) cc_final: 0.7369 (ptt) outliers start: 76 outliers final: 62 residues processed: 435 average time/residue: 1.1929 time to fit residues: 639.2894 Evaluate side-chains 441 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 372 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain B residue 1035 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1035 THR Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 276 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 275 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.0970 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 747 HIS A 771 HIS B 142 GLN B 468 HIS B 747 HIS C 142 GLN C 468 HIS C 747 HIS C 771 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.190505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138109 restraints weight = 36275.694| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.36 r_work: 0.3541 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32252 Z= 0.289 Angle : 0.783 31.557 43716 Z= 0.343 Chirality : 0.066 1.729 4972 Planarity : 0.004 0.055 5324 Dihedral : 13.239 173.731 5844 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.44 % Allowed : 17.70 % Favored : 79.86 % 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: 0.72 (0.14), residues: 3752 helix: 1.01 (0.12), residues: 1884 sheet: -0.12 (0.26), residues: 368 loop : 0.12 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 694 HIS 0.005 0.001 HIS D 753 PHE 0.029 0.002 PHE D 34 TYR 0.021 0.002 TYR A1032 ARG 0.007 0.000 ARG C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12547.57 seconds wall clock time: 226 minutes 19.69 seconds (13579.69 seconds total)