Starting phenix.real_space_refine on Fri Mar 22 08:16:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3l_30983/03_2024/7e3l_30983_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3l_30983/03_2024/7e3l_30983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3l_30983/03_2024/7e3l_30983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3l_30983/03_2024/7e3l_30983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3l_30983/03_2024/7e3l_30983_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3l_30983/03_2024/7e3l_30983_neut.pdb" } resolution = 3.6 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= 0.035 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: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 20739 2.51 5 N 5461 2.21 5 O 6317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 214": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 214": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32639 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7564 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7562 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 7573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7573 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1604 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1604 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1604 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 17.77, per 1000 atoms: 0.54 Number of scatterers: 32639 At special positions: 0 Unit cell: (133.66, 134.48, 261.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 6317 8.00 N 5461 7.00 C 20739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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 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=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.27 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 H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " Time building additional restraints: 12.09 Conformation dependent library (CDL) restraints added in 6.4 seconds 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 80 sheets defined 20.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.747A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.044A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.242A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.637A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.623A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.266A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.314A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' 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 removed outlier: 3.665A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.832A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.527A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.747A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.044A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.241A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.509A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.223A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.720A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.255A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' 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 removed outlier: 3.644A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.786A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.747A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.044A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.242A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.637A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.298A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 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 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (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 removed outlier: 3.516A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.675A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.363A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.107A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 195 through 200 removed outlier: 3.608A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 122 through 128 removed outlier: 3.530A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 190 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.107A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 195 through 200 removed outlier: 3.609A pdb=" N GLY F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 122 through 128 removed outlier: 3.529A pdb=" N SER G 128 " --> pdb=" O GLU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.107A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 195 through 200 removed outlier: 3.608A pdb=" N GLY D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.530A pdb=" N SER E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.583A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.019A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.803A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.875A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.920A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.728A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 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 565 through 567 removed outlier: 6.344A 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: 6.591A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 727 removed outlier: 7.206A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.103A 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 788 through 789 removed outlier: 5.717A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.605A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.818A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.831A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.840A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.506A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.732A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AD4, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.832A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.687A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.636A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 727 removed outlier: 7.128A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.739A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.075A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.938A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 52 through 55 removed outlier: 3.902A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.949A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.692A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.041A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.537A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.591A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 727 removed outlier: 7.148A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.889A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.897A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.682A pdb=" N VAL H 208 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 217 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.638A pdb=" N SER L 64 " --> pdb=" O THR L 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.277A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.088A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 146 through 151 removed outlier: 3.542A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN L 148 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU L 196 " --> pdb=" O GLN L 148 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.889A pdb=" N VAL F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AH3, first strand: chain 'F' and resid 130 through 134 removed outlier: 3.897A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 163 through 164 removed outlier: 3.682A pdb=" N VAL F 208 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL F 217 " --> pdb=" O VAL F 208 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.639A pdb=" N SER G 64 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.278A pdb=" N LEU G 11 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 115 through 119 removed outlier: 4.087A pdb=" N SER G 115 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN G 138 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 146 through 151 removed outlier: 3.542A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 148 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU G 196 " --> pdb=" O GLN G 148 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS G 195 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 208 " --> pdb=" O CYS G 195 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AI1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.890A pdb=" N VAL D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AI3, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.896A pdb=" N GLY D 149 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 163 through 164 removed outlier: 3.682A pdb=" N VAL D 208 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 217 " --> pdb=" O VAL D 208 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.639A pdb=" N SER E 64 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.278A pdb=" N LEU E 11 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.087A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.542A pdb=" N LYS E 146 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 148 " --> pdb=" O GLU E 196 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 196 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS E 195 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 208 " --> pdb=" O CYS E 195 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3204 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: 16.48 Time building geometry restraints manager: 13.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10367 1.34 - 1.47: 8501 1.47 - 1.60: 14348 1.60 - 1.73: 0 1.73 - 1.86: 155 Bond restraints: 33371 Sorted by residual: bond pdb=" N ASN G 94 " pdb=" CA ASN G 94 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N ASN L 94 " pdb=" CA ASN L 94 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" N ASN E 94 " pdb=" CA ASN E 94 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" N ASP H 108 " pdb=" CA ASP H 108 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.34e+00 bond pdb=" N ASP D 108 " pdb=" CA ASP D 108 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.24e+00 ... (remaining 33366 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.65: 974 106.65 - 113.50: 18429 113.50 - 120.35: 12038 120.35 - 127.21: 13746 127.21 - 134.06: 298 Bond angle restraints: 45485 Sorted by residual: angle pdb=" O PHE C 329 " pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 121.88 117.23 4.65 7.10e-01 1.98e+00 4.29e+01 angle pdb=" O PHE A 329 " pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 121.88 117.31 4.57 7.10e-01 1.98e+00 4.15e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.40 -7.70 1.22e+00 6.72e-01 3.98e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.72 -7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.56 -6.86 1.22e+00 6.72e-01 3.16e+01 ... (remaining 45480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 18272 17.99 - 35.97: 1442 35.97 - 53.96: 236 53.96 - 71.94: 42 71.94 - 89.93: 44 Dihedral angle restraints: 20036 sinusoidal: 7661 harmonic: 12375 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.44 -86.44 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.80 -85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.71 -85.71 1 1.00e+01 1.00e-02 8.88e+01 ... (remaining 20033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4993 0.104 - 0.209: 267 0.209 - 0.313: 8 0.313 - 0.417: 6 0.417 - 0.522: 2 Chirality restraints: 5276 Sorted by residual: chirality pdb=" CA CYS C 649 " pdb=" N CYS C 649 " pdb=" C CYS C 649 " pdb=" CB CYS C 649 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" CA CYS B 649 " pdb=" N CYS B 649 " pdb=" C CYS B 649 " pdb=" CB CYS B 649 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 5273 not shown) Planarity restraints: 5882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 649 " -0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C CYS B 649 " 0.065 2.00e-02 2.50e+03 pdb=" O CYS B 649 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU B 650 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 649 " 0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C CYS C 649 " -0.065 2.00e-02 2.50e+03 pdb=" O CYS C 649 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU C 650 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 67 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C GLY E 67 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY E 67 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 68 " 0.018 2.00e-02 2.50e+03 ... (remaining 5879 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2876 2.73 - 3.28: 31554 3.28 - 3.82: 49629 3.82 - 4.36: 58540 4.36 - 4.90: 104134 Nonbonded interactions: 246733 Sorted by model distance: nonbonded pdb=" O PRO A1053 " pdb=" NE2 GLN A1054 " model vdw 2.193 2.520 nonbonded pdb=" NH1 ARG C1091 " pdb=" O ASP C1118 " model vdw 2.202 2.520 nonbonded pdb=" OG SER C 721 " pdb=" OG1 THR C1066 " model vdw 2.208 2.440 nonbonded pdb=" O PRO B1053 " pdb=" NE2 GLN B1054 " model vdw 2.210 2.520 nonbonded pdb=" N GLU E 80 " pdb=" OD2 ASP E 83 " model vdw 2.211 2.520 ... (remaining 246728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 130 or (resid 131 through 132 and (name N or na \ me CA or name C or name O or name CB )) or resid 133 through 165 or (resid 166 a \ nd (name N or name CA or name C or name O or name CB )) or resid 167 through 209 \ or (resid 210 and (name N or name CA or name C or name O or name CB )) or resid \ 211 through 616 or (resid 617 and (name N or name CA or name C or name O or nam \ e CB )) or resid 618 through 648 or (resid 649 and (name N or name CA or name C \ or name O or name CB )) or resid 650 through 661 or (resid 662 and (name N or na \ me CA or name C or name O or name CB )) or resid 663 through 670 or (resid 671 t \ hrough 672 and (name N or name CA or name C or name O or name CB )) or resid 673 \ through 982 or (resid 983 and (name N or name CA or name C or name O or name CB \ )) or resid 984 through 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 27 through 89 or (resid 90 and (name N or name CA or name \ C or name O or name CB )) or resid 91 through 130 or (resid 131 through 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 through 190 or \ (resid 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 through 226 or (resid 227 and (name N or name CA or name C or name O or name C \ B )) or resid 228 through 810 or (resid 811 and (name N or name CA or name C or \ name O or name CB )) or resid 813 through 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 through 209 or (resid 2 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 211 through \ 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) or r \ esid 663 through 670 or (resid 671 through 672 and (name N or name CA or name C \ or name O or name CB )) or resid 673 through 737 or (resid 738 and (name N or na \ me CA or name C or name O or name CB )) or resid 739 through 742 or (resid 743 a \ nd (name N or name CA or name C or name O or name CB )) or resid 744 through 748 \ or (resid 749 and (name N or name CA or name C or name O or name CB )) or resid \ 750 through 759 or (resid 760 and (name N or name CA or name C or name O or nam \ e CB )) or resid 761 through 810 or (resid 811 and (name N or name CA or name C \ or name O or name CB )) or resid 813 through 982 or (resid 983 and (name N or na \ me CA or name C or name O or name CB )) or resid 984 through 1147 or resid 1301 \ through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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 group one per residue 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: 11.860 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: 0.050 Extract box with map and model: 29.550 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 89.610 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 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 : 0.006 0.055 33371 Z= 0.413 Angle : 0.877 11.104 45485 Z= 0.521 Chirality : 0.054 0.522 5276 Planarity : 0.005 0.042 5862 Dihedral : 13.393 89.926 11942 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.91 % Favored : 91.00 % Rotamer: Outliers : 0.32 % Allowed : 3.65 % Favored : 96.03 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 4188 helix: -0.92 (0.17), residues: 672 sheet: -1.45 (0.15), residues: 1218 loop : -2.65 (0.11), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 164 HIS 0.012 0.002 HIS L 190 PHE 0.019 0.002 PHE H 132 TYR 0.038 0.002 TYR B 873 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 342 time to evaluate : 4.619 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: C 902 MET cc_start: 0.8644 (mmm) cc_final: 0.8385 (tpt) outliers start: 11 outliers final: 2 residues processed: 350 average time/residue: 0.5847 time to fit residues: 300.7380 Evaluate side-chains 169 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 3.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain G residue 54 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 357 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 331 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 384 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 690 GLN A 762 GLN A 935 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 165 ASN B 394 ASN B 414 GLN B 658 ASN B 690 GLN B 804 GLN B 935 GLN B 992 GLN B1071 GLN B1088 HIS B1106 GLN C 115 GLN C 394 ASN C 414 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 690 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1106 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5399 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33371 Z= 0.335 Angle : 0.656 8.813 45485 Z= 0.344 Chirality : 0.045 0.193 5276 Planarity : 0.005 0.052 5862 Dihedral : 6.092 58.706 4964 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.86 % Allowed : 9.63 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.12), residues: 4188 helix: 0.68 (0.19), residues: 744 sheet: -1.00 (0.15), residues: 1203 loop : -2.09 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.004 0.001 HIS C1083 PHE 0.017 0.002 PHE H 29 TYR 0.021 0.002 TYR C 91 ARG 0.008 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 4.047 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: C 331 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.5137 (p0) outliers start: 30 outliers final: 15 residues processed: 208 average time/residue: 0.5490 time to fit residues: 175.0277 Evaluate side-chains 172 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 207 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 319 optimal weight: 40.0000 chunk 261 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 384 optimal weight: 30.0000 chunk 415 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 381 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 308 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1088 HIS B 317 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 751 ASN C 207 HIS C 498 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1048 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN E 167 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 33371 Z= 0.528 Angle : 0.743 13.052 45485 Z= 0.387 Chirality : 0.047 0.204 5276 Planarity : 0.005 0.054 5862 Dihedral : 6.172 59.545 4961 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.41 % Allowed : 12.50 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.12), residues: 4188 helix: 0.95 (0.19), residues: 726 sheet: -1.00 (0.14), residues: 1248 loop : -1.92 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.022 0.002 HIS D 44 PHE 0.025 0.002 PHE B 643 TYR 0.023 0.002 TYR C 91 ARG 0.008 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 164 time to evaluate : 3.822 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: A 133 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6537 (t80) REVERT: C 226 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8056 (pt) REVERT: L 170 LYS cc_start: 0.2832 (pttp) cc_final: 0.2566 (pttp) REVERT: G 170 LYS cc_start: 0.0719 (pttm) cc_final: 0.0286 (pttm) outliers start: 84 outliers final: 52 residues processed: 241 average time/residue: 0.5001 time to fit residues: 188.9930 Evaluate side-chains 196 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 142 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 380 optimal weight: 20.0000 chunk 289 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 386 optimal weight: 6.9990 chunk 408 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A1048 HIS A1071 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 644 GLN B 658 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33371 Z= 0.206 Angle : 0.565 10.807 45485 Z= 0.293 Chirality : 0.043 0.174 5276 Planarity : 0.004 0.049 5862 Dihedral : 5.461 59.387 4961 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.95 % Allowed : 14.20 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4188 helix: 1.77 (0.20), residues: 729 sheet: -0.82 (0.14), residues: 1305 loop : -1.54 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.003 0.001 HIS C 66 PHE 0.019 0.001 PHE C 490 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 161 time to evaluate : 4.014 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: A 133 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6473 (t80) REVERT: B 613 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7401 (tm130) REVERT: C 779 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7966 (tm-30) REVERT: G 170 LYS cc_start: 0.0533 (pttm) cc_final: 0.0191 (pttm) REVERT: G 188 GLU cc_start: 0.4421 (tp30) cc_final: 0.4167 (tp30) outliers start: 68 outliers final: 36 residues processed: 219 average time/residue: 0.4659 time to fit residues: 161.7599 Evaluate side-chains 181 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 340 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 168 optimal weight: 0.0170 chunk 348 optimal weight: 9.9990 chunk 282 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 366 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 658 ASN B 751 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN G 167 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 33371 Z= 0.386 Angle : 0.628 12.367 45485 Z= 0.323 Chirality : 0.044 0.206 5276 Planarity : 0.004 0.051 5862 Dihedral : 5.504 58.511 4961 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.39 % Allowed : 14.94 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4188 helix: 1.73 (0.19), residues: 729 sheet: -0.81 (0.14), residues: 1311 loop : -1.45 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.005 0.001 HIS F 210 PHE 0.018 0.002 PHE C 490 TYR 0.024 0.002 TYR C 91 ARG 0.004 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 144 time to evaluate : 3.933 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: A 133 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6564 (t80) REVERT: A 495 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: B 1071 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: C 779 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8115 (tm-30) outliers start: 83 outliers final: 59 residues processed: 220 average time/residue: 0.4823 time to fit residues: 168.3372 Evaluate side-chains 201 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 139 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 137 optimal weight: 9.9990 chunk 368 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 409 optimal weight: 40.0000 chunk 339 optimal weight: 30.0000 chunk 189 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1071 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 33371 Z= 0.475 Angle : 0.679 14.367 45485 Z= 0.351 Chirality : 0.046 0.183 5276 Planarity : 0.004 0.052 5862 Dihedral : 5.730 58.792 4961 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.05 % Allowed : 15.69 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4188 helix: 1.74 (0.19), residues: 708 sheet: -0.87 (0.14), residues: 1263 loop : -1.44 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.013 0.001 HIS F 210 PHE 0.020 0.002 PHE A 855 TYR 0.026 0.002 TYR C 91 ARG 0.004 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 143 time to evaluate : 3.990 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: A 133 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6307 (t80) REVERT: A 495 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: B 1071 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: C 779 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8201 (tm-30) outliers start: 106 outliers final: 85 residues processed: 242 average time/residue: 0.4665 time to fit residues: 180.3848 Evaluate side-chains 222 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 134 time to evaluate : 4.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 394 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 407 optimal weight: 0.2980 chunk 255 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 658 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C1071 GLN H 62 GLN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33371 Z= 0.276 Angle : 0.586 13.781 45485 Z= 0.301 Chirality : 0.043 0.167 5276 Planarity : 0.004 0.089 5862 Dihedral : 5.377 59.997 4961 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.33 % Allowed : 16.61 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4188 helix: 2.09 (0.20), residues: 711 sheet: -0.74 (0.14), residues: 1302 loop : -1.33 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.004 0.001 HIS C 66 PHE 0.020 0.001 PHE C 490 TYR 0.018 0.001 TYR C 91 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 142 time to evaluate : 3.958 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: A 133 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6288 (t80) REVERT: A 495 TYR cc_start: 0.6014 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: B 1071 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: L 170 LYS cc_start: 0.2456 (pttp) cc_final: 0.2115 (pttm) REVERT: F 2 MET cc_start: 0.4065 (ttt) cc_final: 0.3851 (ttt) outliers start: 81 outliers final: 66 residues processed: 219 average time/residue: 0.4687 time to fit residues: 163.5459 Evaluate side-chains 202 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 133 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 252 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 320 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 33371 Z= 0.323 Angle : 0.609 14.983 45485 Z= 0.311 Chirality : 0.044 0.166 5276 Planarity : 0.004 0.066 5862 Dihedral : 5.375 58.794 4961 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.56 % Allowed : 16.95 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4188 helix: 2.09 (0.20), residues: 711 sheet: -0.83 (0.14), residues: 1281 loop : -1.21 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS F 174 PHE 0.019 0.001 PHE C 490 TYR 0.021 0.001 TYR C 91 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 132 time to evaluate : 3.887 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: A 133 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6355 (t80) REVERT: A 495 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: B 165 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.6956 (p0) REVERT: B 1071 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: C 779 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8132 (tm-30) REVERT: L 170 LYS cc_start: 0.2646 (pttp) cc_final: 0.2319 (pttm) outliers start: 89 outliers final: 79 residues processed: 219 average time/residue: 0.4651 time to fit residues: 163.3818 Evaluate side-chains 212 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 129 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 370 optimal weight: 5.9990 chunk 390 optimal weight: 50.0000 chunk 356 optimal weight: 20.0000 chunk 379 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 298 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 359 optimal weight: 40.0000 chunk 378 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 33371 Z= 0.556 Angle : 0.734 15.444 45485 Z= 0.377 Chirality : 0.047 0.194 5276 Planarity : 0.005 0.059 5862 Dihedral : 5.832 58.188 4961 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.96 % Allowed : 16.90 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4188 helix: 1.68 (0.19), residues: 711 sheet: -0.98 (0.14), residues: 1293 loop : -1.32 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 36 HIS 0.005 0.001 HIS C 207 PHE 0.022 0.002 PHE A 855 TYR 0.029 0.002 TYR C 91 ARG 0.004 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 133 time to evaluate : 3.715 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: A 133 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6338 (t80) REVERT: A 495 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5569 (m-80) REVERT: B 1071 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: C 226 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8174 (pt) REVERT: C 779 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8308 (tm-30) REVERT: L 170 LYS cc_start: 0.2488 (pttp) cc_final: 0.2177 (pttm) REVERT: E 63 PHE cc_start: 0.1470 (OUTLIER) cc_final: 0.1113 (m-80) outliers start: 103 outliers final: 90 residues processed: 232 average time/residue: 0.4661 time to fit residues: 173.7869 Evaluate side-chains 224 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 129 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 249 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 245 optimal weight: 0.0050 chunk 190 optimal weight: 0.8980 chunk 279 optimal weight: 0.8980 chunk 421 optimal weight: 30.0000 chunk 387 optimal weight: 30.0000 chunk 335 optimal weight: 5.9990 chunk 34 optimal weight: 0.0010 chunk 259 optimal weight: 0.9980 chunk 205 optimal weight: 0.8980 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 388 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 GLN F 181 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33371 Z= 0.166 Angle : 0.571 14.693 45485 Z= 0.293 Chirality : 0.043 0.165 5276 Planarity : 0.004 0.055 5862 Dihedral : 5.156 59.120 4961 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.38 % Allowed : 18.36 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4188 helix: 2.32 (0.20), residues: 711 sheet: -0.70 (0.14), residues: 1311 loop : -1.11 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS C 66 PHE 0.022 0.001 PHE C 490 TYR 0.018 0.001 TYR A 365 ARG 0.005 0.000 ARG E 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 147 time to evaluate : 3.956 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: A 133 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6392 (t80) REVERT: A 495 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5584 (m-80) REVERT: A 1005 GLN cc_start: 0.8456 (tp40) cc_final: 0.8244 (mm110) REVERT: B 1071 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: L 170 LYS cc_start: 0.2350 (pttp) cc_final: 0.2029 (pttm) REVERT: E 63 PHE cc_start: 0.1138 (OUTLIER) cc_final: 0.0885 (m-80) outliers start: 48 outliers final: 36 residues processed: 190 average time/residue: 0.5090 time to fit residues: 151.3876 Evaluate side-chains 178 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.9189 > 50: distance: 31 - 89: 23.849 distance: 34 - 86: 6.517 distance: 43 - 74: 18.003 distance: 46 - 71: 10.649 distance: 63 - 65: 17.282 distance: 65 - 66: 34.078 distance: 65 - 208: 17.090 distance: 66 - 67: 43.922 distance: 66 - 69: 18.283 distance: 67 - 68: 20.456 distance: 67 - 71: 34.178 distance: 68 - 205: 28.108 distance: 69 - 70: 12.184 distance: 70 - 212: 20.012 distance: 71 - 72: 25.318 distance: 72 - 73: 32.122 distance: 72 - 75: 24.122 distance: 73 - 74: 25.583 distance: 73 - 79: 22.946 distance: 75 - 76: 17.666 distance: 76 - 77: 17.990 distance: 76 - 78: 11.928 distance: 79 - 80: 14.644 distance: 79 - 194: 9.423 distance: 80 - 81: 13.093 distance: 80 - 83: 10.343 distance: 81 - 82: 13.465 distance: 81 - 86: 12.998 distance: 82 - 191: 15.677 distance: 83 - 84: 5.527 distance: 83 - 85: 5.247 distance: 86 - 87: 10.742 distance: 87 - 88: 13.496 distance: 87 - 90: 11.014 distance: 88 - 89: 26.273 distance: 88 - 95: 19.699 distance: 90 - 91: 5.396 distance: 91 - 92: 3.463 distance: 92 - 93: 3.195 distance: 93 - 94: 6.601 distance: 95 - 96: 12.566 distance: 95 - 176: 22.879 distance: 96 - 97: 31.391 distance: 96 - 99: 21.400 distance: 97 - 98: 31.144 distance: 97 - 100: 40.812 distance: 100 - 101: 5.409 distance: 101 - 102: 31.029 distance: 101 - 104: 24.924 distance: 102 - 103: 46.183 distance: 102 - 112: 21.064 distance: 104 - 105: 25.619 distance: 105 - 106: 10.978 distance: 105 - 107: 9.839 distance: 106 - 108: 12.909 distance: 107 - 109: 5.663 distance: 108 - 110: 10.757 distance: 109 - 110: 6.357 distance: 110 - 111: 8.099 distance: 112 - 113: 7.347 distance: 113 - 114: 23.657 distance: 113 - 116: 15.135 distance: 114 - 115: 29.120 distance: 114 - 123: 16.952 distance: 116 - 117: 18.485 distance: 117 - 118: 10.625 distance: 117 - 119: 11.321 distance: 118 - 120: 7.118 distance: 119 - 121: 7.706 distance: 120 - 122: 7.128 distance: 121 - 122: 14.097 distance: 123 - 124: 16.326 distance: 123 - 129: 21.993 distance: 124 - 125: 21.686 distance: 124 - 127: 14.912 distance: 125 - 126: 36.845 distance: 125 - 130: 40.218 distance: 127 - 128: 19.482 distance: 128 - 129: 21.163 distance: 130 - 131: 11.048 distance: 131 - 132: 37.518 distance: 131 - 134: 36.781 distance: 132 - 133: 25.783 distance: 132 - 139: 17.565 distance: 134 - 135: 22.907 distance: 135 - 136: 24.060 distance: 136 - 137: 27.513 distance: 136 - 138: 49.049 distance: 139 - 140: 17.605 distance: 139 - 145: 19.408 distance: 140 - 141: 18.787 distance: 140 - 143: 24.699 distance: 141 - 142: 13.561 distance: 141 - 146: 15.708 distance: 144 - 145: 27.719