Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 02:06:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/04_2023/7f75_31485.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/04_2023/7f75_31485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/04_2023/7f75_31485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/04_2023/7f75_31485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/04_2023/7f75_31485.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/04_2023/7f75_31485.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 121 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 16516 2.51 5 N 4697 2.21 5 O 5488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C ASP 399": "OD1" <-> "OD2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C GLU 735": "OE1" <-> "OE2" Residue "C TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "C GLU 867": "OE1" <-> "OE2" Residue "C ARG 895": "NH1" <-> "NH2" Residue "C ARG 917": "NH1" <-> "NH2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C TYR 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 999": "OD1" <-> "OD2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1019": "OD1" <-> "OD2" Residue "C PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1027": "OD1" <-> "OD2" Residue "C ASP 1046": "OD1" <-> "OD2" Residue "C ARG 1074": "NH1" <-> "NH2" Residue "C GLU 1134": "OE1" <-> "OE2" Residue "C ASP 1148": "OD1" <-> "OD2" Residue "C GLU 1150": "OE1" <-> "OE2" Residue "C GLU 1151": "OE1" <-> "OE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 209": "NH1" <-> "NH2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D ASP 453": "OD1" <-> "OD2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D ASP 641": "OD1" <-> "OD2" Residue "D ASP 662": "OD1" <-> "OD2" Residue "D GLU 675": "OE1" <-> "OE2" Residue "D ARG 697": "NH1" <-> "NH2" Residue "D ASP 710": "OD1" <-> "OD2" Residue "D ASP 721": "OD1" <-> "OD2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 846": "NH1" <-> "NH2" Residue "D GLU 929": "OE1" <-> "OE2" Residue "D GLU 1068": "OE1" <-> "OE2" Residue "D ARG 1072": "NH1" <-> "NH2" Residue "D GLU 1163": "OE1" <-> "OE2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "F ASP 275": "OD1" <-> "OD2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F ARG 343": "NH1" <-> "NH2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G ASP 97": "OD1" <-> "OD2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "I GLU 304": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 26887 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1540 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1538 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 8041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8041 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 188} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1080} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 939 Unresolved non-hydrogen angles: 1163 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 15, 'ASN:plan1': 8, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 598 Chain: "D" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1142, 7891 Classifications: {'peptide': 1142} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 1090} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1128 Unresolved non-hydrogen angles: 1406 Unresolved non-hydrogen dihedrals: 928 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 10, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 40, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 638 Chain: "E" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 405 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2047 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 114 Chain: "H" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 542 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1077 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 120} Chain: "I" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1225 Classifications: {'DNA': 59} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 58} Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1285 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 763 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11575 SG CYS D 60 113.745 84.384 50.519 1.00 86.06 S ATOM 11682 SG CYS D 75 117.734 85.878 50.564 1.00 85.04 S ATOM 16813 SG CYS D 818 81.683 91.755 106.987 1.00 16.08 S ATOM 17262 SG CYS D 892 80.681 91.784 103.478 1.00 9.76 S ATOM 17305 SG CYS D 899 81.475 88.710 105.117 1.00 7.66 S ATOM 17321 SG CYS D 902 77.754 89.714 106.610 1.00 8.60 S Time building chain proxies: 14.16, per 1000 atoms: 0.53 Number of scatterers: 26887 At special positions: 0 Unit cell: (150.305, 156.84, 139.849, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 62 16.00 P 121 15.00 Mg 1 11.99 O 5488 8.00 N 4697 7.00 C 16516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 13 " distance=2.40 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.30 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 60 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 902 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 892 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 899 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 818 " Number of angles added : 6 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6326 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 39 sheets defined 39.9% alpha, 8.9% beta 37 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 7.51 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.893A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.942A pdb=" N ILE B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.790A pdb=" N ILE B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.905A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 77 through 85 removed outlier: 4.197A pdb=" N LYS C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.878A pdb=" N ASP C 222 " --> pdb=" O ASN C 219 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS C 223 " --> pdb=" O THR C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 223' Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.951A pdb=" N ALA C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.501A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.535A pdb=" N ASN C 283 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.759A pdb=" N ARG C 407 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 436 removed outlier: 4.357A pdb=" N ARG C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.804A pdb=" N TYR C 572 " --> pdb=" O GLU C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 removed outlier: 4.091A pdb=" N VAL C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 628 through 632 removed outlier: 3.504A pdb=" N ASN C 631 " --> pdb=" O PHE C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.626A pdb=" N MET C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 968 through 983 Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'C' and resid 1004 through 1009 Processing helix chain 'C' and resid 1043 through 1048 removed outlier: 4.106A pdb=" N LYS C1047 " --> pdb=" O MET C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1086 removed outlier: 3.677A pdb=" N TYR C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1097 Processing helix chain 'C' and resid 1105 through 1116 removed outlier: 3.900A pdb=" N VAL C1114 " --> pdb=" O TYR C1110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C1115 " --> pdb=" O GLU C1111 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1139 removed outlier: 3.809A pdb=" N GLY C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.631A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG D 91 " --> pdb=" O ARG D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.956A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 4.071A pdb=" N ARG D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.889A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.544A pdb=" N ILE D 227 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 3.542A pdb=" N ARG D 239 " --> pdb=" O PRO D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 273 removed outlier: 4.020A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 Processing helix chain 'D' and resid 298 through 301 removed outlier: 4.258A pdb=" N ARG D 301 " --> pdb=" O ASN D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.512A pdb=" N LEU D 320 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 366 through 378 Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 396 through 405 removed outlier: 4.022A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.559A pdb=" N GLN D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.701A pdb=" N GLY D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 562 through 568 Processing helix chain 'D' and resid 604 through 608 removed outlier: 4.473A pdb=" N ALA D 607 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN D 608 " --> pdb=" O VAL D 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 604 through 608' Processing helix chain 'D' and resid 616 through 632 Processing helix chain 'D' and resid 635 through 655 removed outlier: 3.782A pdb=" N LYS D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 689 removed outlier: 4.246A pdb=" N GLN D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 671 " --> pdb=" O ASP D 667 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 718 removed outlier: 4.434A pdb=" N ILE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 737 through 743 removed outlier: 4.172A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 808 removed outlier: 4.293A pdb=" N HIS D 781 " --> pdb=" O PHE D 777 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 843 Processing helix chain 'D' and resid 870 through 875 Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.634A pdb=" N THR D 891 " --> pdb=" O SER D 888 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 892 " --> pdb=" O ALA D 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 888 through 892' Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 919 through 929 removed outlier: 3.540A pdb=" N GLU D 929 " --> pdb=" O GLN D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 932 No H-bonds generated for 'chain 'D' and resid 930 through 932' Processing helix chain 'D' and resid 953 through 962 Processing helix chain 'D' and resid 1039 through 1059 removed outlier: 3.756A pdb=" N GLN D1052 " --> pdb=" O LEU D1048 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS D1053 " --> pdb=" O HIS D1049 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D1055 " --> pdb=" O VAL D1051 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET D1057 " --> pdb=" O LYS D1053 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1073 removed outlier: 3.995A pdb=" N GLU D1068 " --> pdb=" O ASP D1064 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL D1069 " --> pdb=" O LYS D1065 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N MET D1070 " --> pdb=" O HIS D1066 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1093 through 1102 Processing helix chain 'D' and resid 1103 through 1108 removed outlier: 4.209A pdb=" N LEU D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1129 removed outlier: 3.521A pdb=" N SER D1127 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D1128 " --> pdb=" O THR D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1138 Processing helix chain 'D' and resid 1141 through 1153 Processing helix chain 'D' and resid 1162 through 1168 Processing helix chain 'E' and resid 6 through 14 removed outlier: 4.089A pdb=" N ASN E 11 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS E 12 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 removed outlier: 4.682A pdb=" N THR E 21 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 116 through 130 Processing helix chain 'F' and resid 133 through 153 removed outlier: 4.277A pdb=" N GLU F 140 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG F 152 " --> pdb=" O SER F 148 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 186 through 205 removed outlier: 4.056A pdb=" N TRP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TRP F 193 " --> pdb=" O TYR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 234 removed outlier: 3.717A pdb=" N THR F 218 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 4.005A pdb=" N ASP F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.988A pdb=" N ASP F 280 " --> pdb=" O HIS F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 313 through 323 removed outlier: 4.105A pdb=" N VAL F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'F' and resid 342 through 359 removed outlier: 4.073A pdb=" N ILE F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.660A pdb=" N SER F 363 " --> pdb=" O HIS F 359 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 364 " --> pdb=" O PRO F 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 359 through 364' Processing helix chain 'F' and resid 365 through 370 removed outlier: 5.643A pdb=" N ASP F 368 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 370 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 52 through 61 removed outlier: 3.534A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER H 61 " --> pdb=" O TYR H 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 52 through 57 removed outlier: 4.008A pdb=" N ILE G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 68 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.631A pdb=" N LEU G 114 " --> pdb=" O ARG G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 removed outlier: 4.016A pdb=" N PHE G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN G 122 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G 123 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 125 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 250 Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.848A pdb=" N GLU I 255 " --> pdb=" O THR I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 268 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 281 through 287 Processing helix chain 'I' and resid 292 through 306 Processing helix chain 'L' and resid 7 through 14 Processing helix chain 'L' and resid 15 through 28 removed outlier: 3.643A pdb=" N ILE L 19 " --> pdb=" O ALA L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 44 Processing helix chain 'L' and resid 51 through 65 Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 85 through 92 removed outlier: 3.777A pdb=" N GLU L 89 " --> pdb=" O ASP L 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.565A pdb=" N LYS A 8 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 181 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.702A pdb=" N ALA A 52 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 143 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 102 removed outlier: 3.791A pdb=" N PHE A 136 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 108 removed outlier: 6.582A pdb=" N GLY A 105 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR A 129 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 107 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.644A pdb=" N THR A 149 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 168 " --> pdb=" O THR A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.628A pdb=" N GLU B 181 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 142 removed outlier: 6.246A pdb=" N ARG B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 56 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.724A pdb=" N THR B 149 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 168 " --> pdb=" O THR B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 15 through 16 removed outlier: 6.030A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.973A pdb=" N ARG C 97 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 92 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 137 removed outlier: 6.816A pdb=" N SER C 136 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER C 530 " --> pdb=" O CYS C 515 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 144 through 148 removed outlier: 3.600A pdb=" N LEU C 170 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 171 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 190 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.513A pdb=" N ILE C 347 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 544 through 545 Processing sheet with id=AC1, first strand: chain 'C' and resid 547 through 549 Processing sheet with id=AC2, first strand: chain 'C' and resid 674 through 675 Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 685 removed outlier: 3.541A pdb=" N ILE C 681 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP C 691 " --> pdb=" O GLU C 683 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL C 685 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 690 " --> pdb=" O TYR C 710 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 710 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL C 692 " --> pdb=" O ASP C 708 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 708 " --> pdb=" O VAL C 692 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 749 removed outlier: 3.635A pdb=" N GLU C 752 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 758 through 763 removed outlier: 4.612A pdb=" N SER C1031 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 774 through 775 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 799 removed outlier: 3.603A pdb=" N GLU C 793 " --> pdb=" O ILE C 913 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 909 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C 907 " --> pdb=" O ALA C 799 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 908 " --> pdb=" O PHE C 893 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 889 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 914 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE C 887 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 808 through 809 Processing sheet with id=AC9, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.562A pdb=" N HIS C1049 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.562A pdb=" N HIS C1049 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1140 through 1143 Processing sheet with id=AD3, first strand: chain 'C' and resid 1145 through 1146 removed outlier: 3.935A pdb=" N GLU C1150 " --> pdb=" O SER C1146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 94 through 101 removed outlier: 10.690A pdb=" N LEU D 97 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ALA D 99 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL D 230 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.913A pdb=" N VAL D 135 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D 169 " --> pdb=" O VAL D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 241 through 243 removed outlier: 6.830A pdb=" N PHE D 249 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 536 through 539 removed outlier: 3.511A pdb=" N THR D 560 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 539 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 558 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 905 through 906 removed outlier: 3.659A pdb=" N SER D 911 " --> pdb=" O ASN D 906 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 977 through 980 removed outlier: 3.501A pdb=" N VAL D 992 " --> pdb=" O VAL D 979 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 21 through 26 removed outlier: 6.873A pdb=" N LYS H 4 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE H 47 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE H 6 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 27 through 31 Processing sheet with id=AE3, first strand: chain 'L' and resid 68 through 69 removed outlier: 3.877A pdb=" N GLY L 77 " --> pdb=" O LEU L 69 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 11.55 Time building geometry restraints manager: 12.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6282 1.33 - 1.45: 5740 1.45 - 1.57: 15163 1.57 - 1.69: 241 1.69 - 1.82: 107 Bond restraints: 27533 Sorted by residual: bond pdb=" C ASP E 3 " pdb=" N PRO E 4 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.20e-03 1.49e+04 3.07e+01 bond pdb=" N PRO G 120 " pdb=" CD PRO G 120 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" C3' DA J 9 " pdb=" O3' DA J 9 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.80e+00 bond pdb=" C GLY C 72 " pdb=" N GLU C 73 " ideal model delta sigma weight residual 1.331 1.286 0.045 2.07e-02 2.33e+03 4.75e+00 bond pdb=" C TYR C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.63e+00 ... (remaining 27528 not shown) Histogram of bond angle deviations from ideal: 97.42 - 105.33: 1028 105.33 - 113.24: 15345 113.24 - 121.14: 13772 121.14 - 129.05: 7662 129.05 - 136.96: 174 Bond angle restraints: 37981 Sorted by residual: angle pdb=" C GLY C1147 " pdb=" N ASP C1148 " pdb=" CA ASP C1148 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.83e+01 angle pdb=" CA LEU C 319 " pdb=" C LEU C 319 " pdb=" N PRO C 320 " ideal model delta sigma weight residual 118.45 113.36 5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" C LEU C 319 " pdb=" N PRO C 320 " pdb=" CA PRO C 320 " ideal model delta sigma weight residual 119.84 126.35 -6.51 1.25e+00 6.40e-01 2.71e+01 angle pdb=" N ILE C 30 " pdb=" CA ILE C 30 " pdb=" C ILE C 30 " ideal model delta sigma weight residual 111.91 107.33 4.58 8.90e-01 1.26e+00 2.64e+01 angle pdb=" C LYS C 101 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " ideal model delta sigma weight residual 122.61 130.30 -7.69 1.56e+00 4.11e-01 2.43e+01 ... (remaining 37976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 15427 35.82 - 71.65: 784 71.65 - 107.47: 29 107.47 - 143.29: 2 143.29 - 179.11: 4 Dihedral angle restraints: 16246 sinusoidal: 6457 harmonic: 9789 Sorted by residual: dihedral pdb=" CB CYS G 10 " pdb=" SG CYS G 10 " pdb=" SG CYS G 13 " pdb=" CB CYS G 13 " ideal model delta sinusoidal sigma weight residual 93.00 34.85 58.15 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N ARG A 30 " pdb=" CA ARG A 30 " ideal model delta harmonic sigma weight residual 180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ALA D 613 " pdb=" C ALA D 613 " pdb=" N PRO D 614 " pdb=" CA PRO D 614 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 16243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3326 0.058 - 0.116: 937 0.116 - 0.174: 209 0.174 - 0.232: 35 0.232 - 0.291: 5 Chirality restraints: 4512 Sorted by residual: chirality pdb=" CB VAL H 14 " pdb=" CA VAL H 14 " pdb=" CG1 VAL H 14 " pdb=" CG2 VAL H 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CG LEU D 331 " pdb=" CB LEU D 331 " pdb=" CD1 LEU D 331 " pdb=" CD2 LEU D 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR D 857 " pdb=" CA THR D 857 " pdb=" OG1 THR D 857 " pdb=" CG2 THR D 857 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4509 not shown) Planarity restraints: 4572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 234 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO D 235 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 276 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO D 277 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 277 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 277 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 953 " 0.048 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO D 954 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 954 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 954 " 0.040 5.00e-02 4.00e+02 ... (remaining 4569 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 120 2.48 - 3.09: 16997 3.09 - 3.69: 40962 3.69 - 4.30: 53670 4.30 - 4.90: 85403 Nonbonded interactions: 197152 Sorted by model distance: nonbonded pdb=" OP2 DG K 17 " pdb=" N2 DG K 17 " model vdw 1.879 2.520 nonbonded pdb=" OD2 ASP D 451 " pdb="MG MG D1501 " model vdw 2.122 2.170 nonbonded pdb=" C2' DA K 21 " pdb=" OP1 DA K 22 " model vdw 2.221 3.440 nonbonded pdb=" OG1 THR C 247 " pdb=" OE1 GLU C 249 " model vdw 2.239 2.440 nonbonded pdb=" O LEU C 41 " pdb=" OH TYR C 69 " model vdw 2.244 2.440 ... (remaining 197147 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 6 through 15 or (resid 16 through 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 40 or (resid 41 through \ 42 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE or name CZ )) or resid 43 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 67 or (resid 68 and (na \ me N or name CA or name C or name O or name CB )) or resid 69 through 97 or (res \ id 98 and (name N or name CA or name C or name O or name CB )) or resid 99 or (r \ esid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 o \ r (resid 102 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 03 through 131 or (resid 132 and (name N or name CA or name C or name O or name \ CB )) or resid 133 through 162 or (resid 163 and (name N or name CA or name C or \ name O or name CB )) or resid 164 through 200 or (resid 201 and (name N or name \ CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 and \ (name N or name CA or name C or name O or name CB )) or resid 208 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB or name CG )) \ or (resid 213 through 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 225)) selection = (chain 'B' and (resid 6 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or (resid 11 and (name N or name CA or name C or name O \ or name CB or name OG1)) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 16 or (resid 17 throug \ h 19 and (name N or name CA or name C or name O or name CB )) or resid 20 throug \ h 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or re \ sid 24 through 29 or (resid 30 and (name N or name CA or name C or name O or nam \ e CB )) or resid 31 through 33 or (resid 34 and (name N or name CA or name C or \ name O or name CB or name OG1)) or resid 35 through 47 or (resid 48 and (name N \ or name CA or name C or name O or name CB )) or resid 49 through 75 or (resid 76 \ through 77 and (name N or name CA or name C or name O or name CB or name OG1)) \ or resid 78 or (resid 79 and (name N or name CA or name C or name O or name CB o \ r name CG1)) or resid 80 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 107 through 121 or (resid 122 an \ d (name N or name CA or name C or name O or name CB )) or resid 123 or (resid 12 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 125 through \ 128 or (resid 129 and (name N or name CA or name C or name O or name CB or name \ OG1)) or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 140 or (resid 141 and (name N or name CA or name C or name O o \ r name CB or name OG1)) or resid 142 through 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or resid 149 through 165 or (resid 166 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 16 \ 7 through 170 or (resid 171 and (name N or name CA or name C or name O or name C \ B or name OG1)) or resid 172 through 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 183 or (resid 184 and (name \ N or name CA or name C or name O or name CB )) or resid 185 through 190 or (res \ id 191 and (name N or name CA or name C or name O or name CB )) or resid 192 thr \ ough 225)) } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.280 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 78.330 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.007 0.072 27533 Z= 0.432 Angle : 0.989 11.961 37981 Z= 0.554 Chirality : 0.058 0.291 4512 Planarity : 0.007 0.076 4572 Dihedral : 19.320 179.115 9917 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.98 % Favored : 90.85 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -4.47 (0.11), residues: 3376 helix: -2.80 (0.11), residues: 1222 sheet: -2.53 (0.25), residues: 318 loop : -3.25 (0.12), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 537 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 581 average time/residue: 0.3974 time to fit residues: 358.3585 Evaluate side-chains 373 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 344 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 15 residues processed: 29 average time/residue: 0.2316 time to fit residues: 17.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 10.0000 chunk 263 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 272 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN C 100 ASN C 280 HIS C 390 ASN C 403 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 646 GLN C 791 HIS C 975 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN D 349 HIS ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 HIS D1044 GLN D1052 GLN D1058 GLN D1164 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 27533 Z= 0.307 Angle : 0.722 15.010 37981 Z= 0.384 Chirality : 0.045 0.315 4512 Planarity : 0.006 0.077 4572 Dihedral : 19.381 179.896 4815 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.80 % Favored : 91.17 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -3.34 (0.13), residues: 3376 helix: -1.29 (0.14), residues: 1242 sheet: -2.33 (0.27), residues: 298 loop : -2.96 (0.12), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 437 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 24 residues processed: 462 average time/residue: 0.3741 time to fit residues: 276.9222 Evaluate side-chains 356 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 332 time to evaluate : 2.922 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 24 average time/residue: 0.2375 time to fit residues: 15.1005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 263 optimal weight: 0.0050 chunk 215 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 342 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 313 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 0.0060 overall best weight: 3.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 646 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 27533 Z= 0.296 Angle : 0.698 10.660 37981 Z= 0.370 Chirality : 0.045 0.229 4512 Planarity : 0.005 0.067 4572 Dihedral : 19.268 179.951 4815 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.75 % Favored : 90.23 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.84 (0.13), residues: 3376 helix: -0.72 (0.15), residues: 1239 sheet: -2.10 (0.27), residues: 290 loop : -2.78 (0.13), residues: 1847 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 405 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 23 residues processed: 426 average time/residue: 0.3568 time to fit residues: 248.3452 Evaluate side-chains 336 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 23 average time/residue: 0.2458 time to fit residues: 14.9341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 317 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 743 GLN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS G 106 ASN L 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 27533 Z= 0.261 Angle : 0.655 11.950 37981 Z= 0.347 Chirality : 0.044 0.210 4512 Planarity : 0.005 0.058 4572 Dihedral : 19.167 179.840 4815 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.60 % Favored : 90.37 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.54 (0.14), residues: 3376 helix: -0.38 (0.15), residues: 1239 sheet: -1.83 (0.29), residues: 278 loop : -2.70 (0.13), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 416 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 22 residues processed: 435 average time/residue: 0.3716 time to fit residues: 265.1193 Evaluate side-chains 331 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 309 time to evaluate : 3.051 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 22 average time/residue: 0.2464 time to fit residues: 14.3253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 4 optimal weight: 0.0270 chunk 250 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 27533 Z= 0.267 Angle : 0.646 11.882 37981 Z= 0.342 Chirality : 0.043 0.187 4512 Planarity : 0.005 0.060 4572 Dihedral : 19.127 179.910 4815 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.51 % Favored : 90.46 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.43 (0.14), residues: 3376 helix: -0.29 (0.15), residues: 1244 sheet: -1.82 (0.29), residues: 275 loop : -2.63 (0.13), residues: 1857 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 394 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 23 residues processed: 414 average time/residue: 0.3671 time to fit residues: 252.1314 Evaluate side-chains 325 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 302 time to evaluate : 3.246 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 23 average time/residue: 0.2595 time to fit residues: 15.4343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.5980 chunk 302 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 279 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 809 GLN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 27533 Z= 0.165 Angle : 0.585 12.391 37981 Z= 0.307 Chirality : 0.042 0.181 4512 Planarity : 0.004 0.058 4572 Dihedral : 18.989 179.983 4815 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.55 % Favored : 92.42 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.07 (0.14), residues: 3376 helix: 0.04 (0.15), residues: 1233 sheet: -1.48 (0.30), residues: 267 loop : -2.45 (0.13), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 419 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 22 residues processed: 438 average time/residue: 0.3585 time to fit residues: 260.1523 Evaluate side-chains 337 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 315 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 22 average time/residue: 0.2419 time to fit residues: 14.1460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 743 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 27533 Z= 0.309 Angle : 0.674 11.890 37981 Z= 0.357 Chirality : 0.044 0.199 4512 Planarity : 0.005 0.060 4572 Dihedral : 19.015 179.757 4815 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.40 % Favored : 89.57 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.26 (0.14), residues: 3376 helix: -0.20 (0.15), residues: 1245 sheet: -1.50 (0.30), residues: 287 loop : -2.54 (0.13), residues: 1844 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 379 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 23 residues processed: 399 average time/residue: 0.3574 time to fit residues: 237.5934 Evaluate side-chains 320 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 297 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 23 average time/residue: 0.2389 time to fit residues: 14.2326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 263 optimal weight: 0.0040 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 220 HIS B 220 HIS C 287 ASN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 478 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 27533 Z= 0.187 Angle : 0.609 12.455 37981 Z= 0.318 Chirality : 0.042 0.183 4512 Planarity : 0.004 0.056 4572 Dihedral : 18.920 179.168 4815 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.12 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.02 (0.14), residues: 3376 helix: 0.04 (0.15), residues: 1239 sheet: -1.30 (0.31), residues: 278 loop : -2.43 (0.13), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 390 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 22 residues processed: 409 average time/residue: 0.3514 time to fit residues: 239.4348 Evaluate side-chains 328 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 306 time to evaluate : 2.931 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 22 average time/residue: 0.2431 time to fit residues: 14.1864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 1.9990 chunk 321 optimal weight: 0.0030 chunk 293 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 282 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS C 403 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN D 255 ASN D 478 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 27533 Z= 0.198 Angle : 0.611 13.344 37981 Z= 0.319 Chirality : 0.042 0.190 4512 Planarity : 0.004 0.056 4572 Dihedral : 18.846 179.575 4815 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.89 % Favored : 91.08 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.94 (0.14), residues: 3376 helix: 0.09 (0.15), residues: 1245 sheet: -1.18 (0.31), residues: 277 loop : -2.38 (0.14), residues: 1854 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 384 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 22 residues processed: 403 average time/residue: 0.3540 time to fit residues: 238.6105 Evaluate side-chains 323 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 3.180 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 22 average time/residue: 0.2529 time to fit residues: 14.9642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 156 optimal weight: 0.0980 chunk 229 optimal weight: 9.9990 chunk 346 optimal weight: 0.9980 chunk 319 optimal weight: 0.9980 chunk 276 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 213 optimal weight: 0.0970 chunk 169 optimal weight: 2.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 220 HIS C 403 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 478 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 27533 Z= 0.164 Angle : 0.590 12.940 37981 Z= 0.306 Chirality : 0.041 0.195 4512 Planarity : 0.004 0.055 4572 Dihedral : 18.755 179.287 4815 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.71 (0.14), residues: 3376 helix: 0.28 (0.15), residues: 1238 sheet: -0.99 (0.32), residues: 265 loop : -2.25 (0.14), residues: 1873 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 403 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 23 residues processed: 423 average time/residue: 0.3493 time to fit residues: 250.8792 Evaluate side-chains 339 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 316 time to evaluate : 2.920 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 23 average time/residue: 0.2499 time to fit residues: 14.9403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 115 optimal weight: 0.0170 chunk 283 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 478 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131805 restraints weight = 52039.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130761 restraints weight = 89251.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131455 restraints weight = 80906.673| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 27533 Z= 0.231 Angle : 0.634 13.014 37981 Z= 0.330 Chirality : 0.043 0.191 4512 Planarity : 0.004 0.070 4572 Dihedral : 18.764 179.456 4815 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.83 (0.14), residues: 3376 helix: 0.17 (0.15), residues: 1256 sheet: -1.26 (0.31), residues: 286 loop : -2.31 (0.14), residues: 1834 =============================================================================== Job complete usr+sys time: 5226.40 seconds wall clock time: 95 minutes 31.67 seconds (5731.67 seconds total)