Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 01:01:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxq_27067/10_2023/8cxq_27067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxq_27067/10_2023/8cxq_27067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxq_27067/10_2023/8cxq_27067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxq_27067/10_2023/8cxq_27067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxq_27067/10_2023/8cxq_27067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxq_27067/10_2023/8cxq_27067.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 18199 2.51 5 N 4814 2.21 5 O 5450 1.98 5 H 27792 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 56384 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 16926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16926 Classifications: {'peptide': 1100} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1043} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 16937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16937 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 16937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 16937 Classifications: {'peptide': 1100} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1863 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1861 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "F" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1860 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Time building chain proxies: 17.56, per 1000 atoms: 0.31 Number of scatterers: 56384 At special positions: 0 Unit cell: (164.78, 167.99, 195.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 5450 8.00 N 4814 7.00 C 18199 6.00 H 27792 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.54 Conformation dependent library (CDL) restraints added in 4.0 seconds 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 66 sheets defined 23.0% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.140A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.965A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.617A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.930A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.225A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.332A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.899A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.975A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.877A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.564A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.832A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.732A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.574A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.563A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.087A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.991A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.152A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.770A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.683A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.670A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 removed outlier: 4.067A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.789A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.851A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.195A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.309A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.491A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.910A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.863A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.880A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 157 removed outlier: 6.554A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.531A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.000A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 4.009A pdb=" N ASN A 450 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR A 495 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A 452 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN A 493 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.677A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.938A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.692A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.228A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.848A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.848A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.554A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.874A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.795A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 151 through 160 removed outlier: 6.826A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 12.833A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.256A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.989A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.805A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.528A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 448 through 454 removed outlier: 4.085A pdb=" N ASN B 450 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR B 495 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 452 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 493 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.637A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.312A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.773A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.773A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.853A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.565A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.322A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AF1, first strand: chain 'C' and resid 311 through 317 removed outlier: 7.029A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 326 through 328 Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.931A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.942A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 448 through 454 removed outlier: 4.036A pdb=" N ASN C 450 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR C 495 " --> pdb=" O ASN C 450 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU C 452 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN C 493 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.055A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.305A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.730A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.229A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.229A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N CYS D 97 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TRP D 112 " --> pdb=" O CYS D 97 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 99 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.829A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.831A pdb=" N SER E 101 " --> pdb=" O PRO E 109 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG E 103 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.718A pdb=" N GLY F 10 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.718A pdb=" N GLY F 10 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER F 101 " --> pdb=" O PRO F 109 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG F 103 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3144 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: 23.40 Time building geometry restraints manager: 36.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 27771 1.03 - 1.23: 47 1.23 - 1.43: 12542 1.43 - 1.62: 16537 1.62 - 1.82: 165 Bond restraints: 57062 Sorted by residual: bond pdb=" C THR B 588 " pdb=" N PRO B 589 " ideal model delta sigma weight residual 1.331 1.347 -0.016 1.21e-02 6.83e+03 1.78e+00 bond pdb=" CA ASP C 228 " pdb=" CB ASP C 228 " ideal model delta sigma weight residual 1.533 1.513 0.020 1.72e-02 3.38e+03 1.40e+00 bond pdb=" CB VAL C 227 " pdb=" CG2 VAL C 227 " ideal model delta sigma weight residual 1.521 1.558 -0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.332 1.345 -0.014 1.26e-02 6.30e+03 1.19e+00 bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.14e+00 ... (remaining 57057 not shown) Histogram of bond angle deviations from ideal: 72.95 - 85.18: 3 85.18 - 97.40: 0 97.40 - 109.63: 38958 109.63 - 121.85: 53115 121.85 - 134.07: 10641 Bond angle restraints: 102717 Sorted by residual: angle pdb=" C VAL A 16 " pdb=" CA VAL A 16 " pdb=" HA VAL A 16 " ideal model delta sigma weight residual 109.00 72.95 36.05 3.00e+00 1.11e-01 1.44e+02 angle pdb=" N VAL A 16 " pdb=" CA VAL A 16 " pdb=" HA VAL A 16 " ideal model delta sigma weight residual 110.00 75.01 34.99 3.00e+00 1.11e-01 1.36e+02 angle pdb=" CB VAL A 16 " pdb=" CA VAL A 16 " pdb=" HA VAL A 16 " ideal model delta sigma weight residual 109.00 76.13 32.87 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C LEU A 176 " pdb=" N MET A 177 " pdb=" CA MET A 177 " ideal model delta sigma weight residual 121.70 133.57 -11.87 1.80e+00 3.09e-01 4.35e+01 angle pdb=" CB LYS B 528 " pdb=" CG LYS B 528 " pdb=" CD LYS B 528 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 ... (remaining 102712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 22164 17.93 - 35.87: 885 35.87 - 53.80: 135 53.80 - 71.74: 34 71.74 - 89.67: 22 Dihedral angle restraints: 23240 sinusoidal: 10454 harmonic: 12786 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual 93.00 25.40 67.60 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CA PRO A 174 " pdb=" C PRO A 174 " pdb=" N PHE A 175 " pdb=" CA PHE A 175 " ideal model delta harmonic sigma weight residual 180.00 144.04 35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA GLN A 173 " pdb=" C GLN A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta harmonic sigma weight residual -180.00 -145.89 -34.11 0 5.00e+00 4.00e-02 4.65e+01 ... (remaining 23237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3728 0.049 - 0.098: 460 0.098 - 0.146: 293 0.146 - 0.195: 0 0.195 - 0.244: 1 Chirality restraints: 4482 Sorted by residual: chirality pdb=" CA VAL A 16 " pdb=" N VAL A 16 " pdb=" C VAL A 16 " pdb=" CB VAL A 16 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE B 119 " pdb=" N ILE B 119 " pdb=" C ILE B 119 " pdb=" CB ILE B 119 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 4479 not shown) Planarity restraints: 8644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 200 " -0.017 2.00e-02 2.50e+03 1.26e-02 4.73e+00 pdb=" CG TYR C 200 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 200 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 200 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 200 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 200 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR C 200 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 200 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR C 200 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR C 200 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TYR C 200 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 200 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO A 174 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 986 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.024 5.00e-02 4.00e+02 ... (remaining 8641 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 2343 2.18 - 2.78: 113412 2.78 - 3.39: 155545 3.39 - 3.99: 207078 3.99 - 4.60: 317171 Nonbonded interactions: 795549 Sorted by model distance: nonbonded pdb=" O PHE D 47 " pdb="HH11 ARG D 62 " model vdw 1.572 1.850 nonbonded pdb=" H VAL A 16 " pdb=" HA VAL A 16 " model vdw 1.586 1.816 nonbonded pdb=" H MET A 731 " pdb=" OE1 GLN A 774 " model vdw 1.592 1.850 nonbonded pdb=" O VAL B 327 " pdb=" H THR B 531 " model vdw 1.608 1.850 nonbonded pdb=" HZ3 LYS C 825 " pdb=" O THR C 941 " model vdw 1.613 1.850 ... (remaining 795544 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' selection = (chain 'B' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 322 through 527 or (re \ sid 528 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or \ name HZ3)) or resid 529 through 1147)) selection = (chain 'C' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 322 through 527 or (re \ sid 528 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or \ name HZ3)) or resid 529 through 1147)) } ncs_group { reference = (chain 'D' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 14 through 116 or (res \ id 117 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HG2 or name HG3)) or resid 118 or (resid 119 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or na \ me HG21 or name HG22 or name HG23)) or (resid 120 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG \ 11 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 1 \ 21 through 122)) selection = (chain 'E' and (resid 1 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 118 or (re \ sid 119 and (name N or name CA or name C or name O or name CB or name OG1 or nam \ e CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) o \ r (resid 120 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23)) or resid 121 through 122)) selection = (chain 'F' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 14 through 122)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.640 Extract box with map and model: 14.510 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 139.720 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.002 0.039 29270 Z= 0.119 Angle : 0.455 11.868 39844 Z= 0.246 Chirality : 0.042 0.244 4482 Planarity : 0.003 0.059 5180 Dihedral : 10.310 89.672 10458 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 0.22 % Allowed : 0.25 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % Twisted Proline : 0.56 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3642 helix: 2.48 (0.21), residues: 714 sheet: 0.30 (0.18), residues: 870 loop : -0.68 (0.13), residues: 2058 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 248 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 8 residues processed: 254 average time/residue: 2.2797 time to fit residues: 690.4710 Evaluate side-chains 188 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 3.207 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 2 average time/residue: 0.4866 time to fit residues: 5.9513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 174 optimal weight: 0.4980 chunk 213 optimal weight: 0.9980 chunk 332 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A1002 GLN A1106 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29270 Z= 0.327 Angle : 0.516 7.985 39844 Z= 0.276 Chirality : 0.044 0.272 4482 Planarity : 0.003 0.047 5180 Dihedral : 4.036 34.389 3957 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 0.88 % Allowed : 4.09 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % Twisted Proline : 0.56 % Twisted General : 0.03 % 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: -0.03 (0.14), residues: 3642 helix: 2.16 (0.20), residues: 715 sheet: 0.17 (0.17), residues: 838 loop : -0.90 (0.13), residues: 2089 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 208 average time/residue: 2.1043 time to fit residues: 529.9309 Evaluate side-chains 195 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 3.236 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 9 average time/residue: 0.9721 time to fit residues: 16.6455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 30.0000 chunk 359 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 330 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29270 Z= 0.228 Angle : 0.479 7.907 39844 Z= 0.252 Chirality : 0.043 0.267 4482 Planarity : 0.003 0.043 5180 Dihedral : 3.997 33.149 3957 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 0.82 % Allowed : 5.06 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % Twisted Proline : 0.56 % Twisted General : 0.03 % 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: -0.05 (0.14), residues: 3642 helix: 2.13 (0.20), residues: 715 sheet: 0.02 (0.17), residues: 852 loop : -0.84 (0.13), residues: 2075 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 199 average time/residue: 2.2051 time to fit residues: 535.2238 Evaluate side-chains 192 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 3.376 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 8 average time/residue: 0.9942 time to fit residues: 15.7133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 0.6980 chunk 250 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 334 optimal weight: 10.0000 chunk 353 optimal weight: 20.0000 chunk 174 optimal weight: 0.2980 chunk 316 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29270 Z= 0.210 Angle : 0.476 8.340 39844 Z= 0.250 Chirality : 0.043 0.269 4482 Planarity : 0.003 0.041 5180 Dihedral : 3.975 31.528 3957 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 0.82 % Allowed : 5.66 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.10 (0.14), residues: 3642 helix: 2.10 (0.20), residues: 719 sheet: -0.03 (0.17), residues: 860 loop : -0.87 (0.13), residues: 2063 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 204 average time/residue: 2.0974 time to fit residues: 518.3615 Evaluate side-chains 190 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 3.274 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.8892 time to fit residues: 8.1013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 263 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29270 Z= 0.225 Angle : 0.476 7.554 39844 Z= 0.250 Chirality : 0.043 0.272 4482 Planarity : 0.003 0.041 5180 Dihedral : 3.957 29.401 3957 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 0.82 % Allowed : 6.16 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % 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: -0.10 (0.14), residues: 3642 helix: 2.12 (0.20), residues: 712 sheet: -0.09 (0.17), residues: 877 loop : -0.85 (0.13), residues: 2053 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 200 average time/residue: 2.1348 time to fit residues: 519.5449 Evaluate side-chains 192 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 3.265 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.9663 time to fit residues: 12.6228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 5.9990 chunk 318 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 354 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29270 Z= 0.165 Angle : 0.464 7.477 39844 Z= 0.242 Chirality : 0.042 0.270 4482 Planarity : 0.003 0.040 5180 Dihedral : 3.888 27.602 3957 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.82 % Allowed : 6.51 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % 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: -0.05 (0.14), residues: 3642 helix: 2.16 (0.20), residues: 718 sheet: 0.00 (0.17), residues: 856 loop : -0.86 (0.13), residues: 2068 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 196 average time/residue: 2.0854 time to fit residues: 501.2970 Evaluate side-chains 189 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.3351 time to fit residues: 7.7764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 201 optimal weight: 0.9980 chunk 258 optimal weight: 20.0000 chunk 200 optimal weight: 1.9990 chunk 298 optimal weight: 0.3980 chunk 197 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29270 Z= 0.285 Angle : 0.492 8.245 39844 Z= 0.259 Chirality : 0.043 0.273 4482 Planarity : 0.003 0.042 5180 Dihedral : 3.977 26.325 3957 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 0.91 % Allowed : 6.69 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % 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: -0.17 (0.14), residues: 3642 helix: 2.01 (0.20), residues: 719 sheet: -0.00 (0.17), residues: 839 loop : -0.95 (0.13), residues: 2084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 199 average time/residue: 2.0868 time to fit residues: 505.9090 Evaluate side-chains 193 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 3.280 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 6 average time/residue: 1.3738 time to fit residues: 14.9375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.0570 chunk 224 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1010 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29270 Z= 0.172 Angle : 0.470 9.895 39844 Z= 0.245 Chirality : 0.042 0.272 4482 Planarity : 0.003 0.049 5180 Dihedral : 3.906 25.428 3957 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 0.75 % Allowed : 6.95 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % 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: -0.09 (0.14), residues: 3642 helix: 2.13 (0.20), residues: 718 sheet: 0.05 (0.17), residues: 830 loop : -0.91 (0.13), residues: 2094 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 197 average time/residue: 2.0354 time to fit residues: 488.2700 Evaluate side-chains 189 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.5875 time to fit residues: 5.1934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.3980 chunk 337 optimal weight: 20.0000 chunk 308 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 297 optimal weight: 0.7980 chunk 310 optimal weight: 0.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29270 Z= 0.187 Angle : 0.471 7.860 39844 Z= 0.245 Chirality : 0.042 0.272 4482 Planarity : 0.003 0.053 5180 Dihedral : 3.866 24.418 3957 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 0.85 % Allowed : 7.13 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % 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: -0.06 (0.14), residues: 3642 helix: 2.16 (0.20), residues: 718 sheet: 0.09 (0.18), residues: 819 loop : -0.89 (0.13), residues: 2105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 200 average time/residue: 2.0990 time to fit residues: 515.1932 Evaluate side-chains 186 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 3.290 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.3884 time to fit residues: 7.9099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 164 optimal weight: 0.2980 chunk 241 optimal weight: 4.9990 chunk 364 optimal weight: 0.7980 chunk 335 optimal weight: 6.9990 chunk 290 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 224 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29270 Z= 0.155 Angle : 0.468 9.895 39844 Z= 0.242 Chirality : 0.042 0.271 4482 Planarity : 0.003 0.056 5180 Dihedral : 3.822 23.310 3957 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 0.63 % Allowed : 7.39 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % 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: -0.00 (0.14), residues: 3642 helix: 2.22 (0.20), residues: 718 sheet: 0.05 (0.17), residues: 837 loop : -0.84 (0.13), residues: 2087 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 188 average time/residue: 2.0476 time to fit residues: 471.8624 Evaluate side-chains 184 residues out of total 3186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 3.270 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 4.2373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 7.9990 chunk 309 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 267 optimal weight: 8.9990 chunk 42 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 290 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.166070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.092186 restraints weight = 147830.170| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.86 r_work: 0.3190 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29270 Z= 0.281 Angle : 0.492 7.802 39844 Z= 0.259 Chirality : 0.043 0.273 4482 Planarity : 0.003 0.098 5180 Dihedral : 3.916 22.673 3957 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 0.72 % Allowed : 7.45 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.03 % 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: -0.13 (0.14), residues: 3642 helix: 2.12 (0.20), residues: 713 sheet: -0.02 (0.17), residues: 835 loop : -0.92 (0.13), residues: 2094 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15145.14 seconds wall clock time: 261 minutes 16.74 seconds (15676.74 seconds total)