Starting phenix.real_space_refine on Tue Feb 20 05:04:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/02_2024/7f75_31485.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/02_2024/7f75_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_31485/02_2024/7f75_31485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/02_2024/7f75_31485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/02_2024/7f75_31485.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f75_31485/02_2024/7f75_31485.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 16.43, per 1000 atoms: 0.61 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: 10.19 Conformation dependent library (CDL) restraints added in 4.9 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: 8.58 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: 12.46 Time building geometry restraints manager: 11.06 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: 15539 35.82 - 71.65: 814 71.65 - 107.47: 29 107.47 - 143.29: 2 143.29 - 179.11: 4 Dihedral angle restraints: 16388 sinusoidal: 6599 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 16385 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: 1.250 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: 4.130 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 82.940 Find NCS groups from input model: 1.170 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.930 ------------------------------------------------------------------------------- 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 : 19.489 179.115 10059 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 % Allowed : 11.45 % Favored : 86.30 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 105 HIS 0.009 0.002 HIS C 862 PHE 0.036 0.003 PHE C 420 TYR 0.022 0.003 TYR C 946 ARG 0.011 0.001 ARG C 928 *********************** 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 : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.9160 (p) cc_final: 0.8958 (p) REVERT: A 64 GLU cc_start: 0.7429 (pt0) cc_final: 0.6805 (pp20) REVERT: A 72 VAL cc_start: 0.8987 (m) cc_final: 0.8607 (p) REVERT: B 187 GLN cc_start: 0.7578 (pm20) cc_final: 0.7207 (pt0) REVERT: B 190 ASN cc_start: 0.7967 (t0) cc_final: 0.7663 (t0) REVERT: C 89 SER cc_start: 0.9323 (m) cc_final: 0.8972 (p) REVERT: C 131 GLU cc_start: 0.7150 (tt0) cc_final: 0.6893 (tt0) REVERT: C 459 LYS cc_start: 0.7720 (mmtp) cc_final: 0.7505 (mmmt) REVERT: C 966 MET cc_start: 0.8348 (mtm) cc_final: 0.7987 (ptp) REVERT: C 1001 TRP cc_start: 0.8587 (m100) cc_final: 0.8172 (m100) REVERT: C 1074 ARG cc_start: 0.7565 (mpt-90) cc_final: 0.7130 (ttt90) REVERT: C 1081 TRP cc_start: 0.8504 (m-10) cc_final: 0.8275 (m-10) REVERT: D 8 GLU cc_start: 0.6562 (tm-30) cc_final: 0.6096 (tm-30) REVERT: D 18 ASP cc_start: 0.6860 (m-30) cc_final: 0.6485 (t70) REVERT: D 116 LEU cc_start: 0.7915 (pp) cc_final: 0.7451 (mt) REVERT: D 210 LEU cc_start: 0.8851 (tp) cc_final: 0.8599 (tp) REVERT: D 329 GLN cc_start: 0.6676 (mt0) cc_final: 0.5668 (tm-30) REVERT: D 455 MET cc_start: 0.8658 (ttm) cc_final: 0.8374 (ttm) REVERT: D 478 ASN cc_start: 0.7625 (m110) cc_final: 0.7421 (m110) REVERT: D 521 GLU cc_start: 0.7710 (pm20) cc_final: 0.6863 (tm-30) REVERT: D 1154 LYS cc_start: 0.8647 (tttt) cc_final: 0.8233 (ttmm) REVERT: F 293 HIS cc_start: 0.4763 (OUTLIER) cc_final: 0.4362 (t70) REVERT: F 312 ASP cc_start: 0.6696 (m-30) cc_final: 0.5824 (p0) REVERT: H 50 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8205 (p) REVERT: H 56 GLU cc_start: 0.8084 (tp30) cc_final: 0.7766 (tp30) REVERT: G 37 LEU cc_start: 0.7094 (mt) cc_final: 0.5926 (mt) REVERT: G 45 ILE cc_start: 0.7545 (mt) cc_final: 0.7196 (mt) REVERT: G 51 ASP cc_start: 0.6956 (m-30) cc_final: 0.6607 (t0) REVERT: G 68 ASN cc_start: 0.4210 (m-40) cc_final: 0.3067 (p0) REVERT: G 102 GLN cc_start: 0.7371 (tp40) cc_final: 0.7051 (tt0) REVERT: I 266 LEU cc_start: 0.4693 (mt) cc_final: 0.4374 (pp) REVERT: L 11 LEU cc_start: 0.5294 (mt) cc_final: 0.5082 (pt) REVERT: L 23 LEU cc_start: 0.5940 (mt) cc_final: 0.5217 (mt) outliers start: 51 outliers final: 29 residues processed: 581 average time/residue: 0.4052 time to fit residues: 365.2253 Evaluate side-chains 392 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 361 time to evaluate : 2.992 ------------------------------------------------------------------------------- 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: 0.7980 chunk 177 optimal weight: 8.9990 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: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 478 ASN 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27533 Z= 0.305 Angle : 0.710 8.605 37981 Z= 0.381 Chirality : 0.045 0.201 4512 Planarity : 0.006 0.076 4572 Dihedral : 19.579 179.995 4957 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.00 % Favored : 90.97 % Rotamer: Outliers : 1.06 % Allowed : 8.13 % Favored : 90.80 % 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: -3.30 (0.13), residues: 3376 helix: -1.26 (0.14), residues: 1247 sheet: -2.30 (0.27), residues: 298 loop : -2.94 (0.12), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 19 HIS 0.006 0.001 HIS D 419 PHE 0.028 0.002 PHE D 648 TYR 0.018 0.002 TYR C 610 ARG 0.014 0.001 ARG C 434 *********************** 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 463 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 439 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9528 (m) cc_final: 0.9264 (p) REVERT: A 64 GLU cc_start: 0.7312 (pt0) cc_final: 0.6510 (pp20) REVERT: B 187 GLN cc_start: 0.7594 (pm20) cc_final: 0.7313 (pt0) REVERT: C 76 TYR cc_start: 0.7055 (m-80) cc_final: 0.6297 (m-80) REVERT: C 84 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.7296 (mpt180) REVERT: C 131 GLU cc_start: 0.7333 (tt0) cc_final: 0.6974 (tt0) REVERT: C 401 ILE cc_start: 0.8855 (pt) cc_final: 0.8447 (mp) REVERT: C 564 LEU cc_start: 0.9320 (tp) cc_final: 0.9014 (tp) REVERT: C 644 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: C 740 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8594 (tt0) REVERT: C 966 MET cc_start: 0.8472 (mtm) cc_final: 0.8254 (mtm) REVERT: C 1001 TRP cc_start: 0.8500 (m100) cc_final: 0.8081 (m100) REVERT: C 1074 ARG cc_start: 0.7618 (mpt-90) cc_final: 0.7099 (ttt90) REVERT: C 1078 MET cc_start: 0.8099 (mtt) cc_final: 0.7843 (mtt) REVERT: D 116 LEU cc_start: 0.7983 (pp) cc_final: 0.7401 (mt) REVERT: D 181 ASP cc_start: 0.7583 (p0) cc_final: 0.7302 (p0) REVERT: D 329 GLN cc_start: 0.6448 (mt0) cc_final: 0.5422 (tm-30) REVERT: D 344 ILE cc_start: 0.9594 (mp) cc_final: 0.9378 (mt) REVERT: D 517 LYS cc_start: 0.8480 (mttp) cc_final: 0.8146 (mtpp) REVERT: D 1154 LYS cc_start: 0.8668 (tttt) cc_final: 0.8352 (ttmm) REVERT: H 36 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8121 (mtpt) REVERT: H 58 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7702 (mm-30) REVERT: G 45 ILE cc_start: 0.7476 (mt) cc_final: 0.7214 (mt) REVERT: G 51 ASP cc_start: 0.7100 (m-30) cc_final: 0.6854 (t0) REVERT: G 102 GLN cc_start: 0.7545 (tp40) cc_final: 0.7309 (tt0) REVERT: L 11 LEU cc_start: 0.5706 (mt) cc_final: 0.5232 (pt) REVERT: L 23 LEU cc_start: 0.6022 (mt) cc_final: 0.5448 (mt) outliers start: 24 outliers final: 22 residues processed: 460 average time/residue: 0.3671 time to fit residues: 270.1472 Evaluate side-chains 366 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 343 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 5.9990 chunk 263 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 316 optimal weight: 30.0000 chunk 342 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 324 GLN ** 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** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27533 Z= 0.347 Angle : 0.735 10.971 37981 Z= 0.390 Chirality : 0.046 0.225 4512 Planarity : 0.005 0.069 4572 Dihedral : 19.501 179.885 4957 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.22 % Favored : 89.75 % Rotamer: Outliers : 1.02 % Allowed : 8.22 % Favored : 90.76 % 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: -2.88 (0.13), residues: 3376 helix: -0.73 (0.15), residues: 1232 sheet: -2.27 (0.27), residues: 298 loop : -2.80 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 105 HIS 0.009 0.002 HIS F 214 PHE 0.023 0.002 PHE C 420 TYR 0.018 0.002 TYR D 501 ARG 0.007 0.001 ARG D 697 *********************** 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 424 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 401 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9558 (m) cc_final: 0.9285 (p) REVERT: C 131 GLU cc_start: 0.7340 (tt0) cc_final: 0.6990 (tt0) REVERT: C 401 ILE cc_start: 0.8756 (pt) cc_final: 0.8421 (mp) REVERT: C 1001 TRP cc_start: 0.8450 (m100) cc_final: 0.8006 (m100) REVERT: C 1074 ARG cc_start: 0.7743 (mpt-90) cc_final: 0.7094 (ttt90) REVERT: C 1078 MET cc_start: 0.7993 (mtt) cc_final: 0.7664 (mtt) REVERT: D 116 LEU cc_start: 0.7964 (pp) cc_final: 0.7315 (mt) REVERT: D 137 THR cc_start: 0.8469 (p) cc_final: 0.8164 (p) REVERT: D 181 ASP cc_start: 0.7726 (p0) cc_final: 0.7499 (p0) REVERT: D 290 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7076 (tm-30) REVERT: D 329 GLN cc_start: 0.6709 (mt0) cc_final: 0.5773 (tm-30) REVERT: D 344 ILE cc_start: 0.9661 (mp) cc_final: 0.9391 (mt) REVERT: D 455 MET cc_start: 0.8384 (ttm) cc_final: 0.8075 (ttm) REVERT: D 517 LYS cc_start: 0.8582 (mttp) cc_final: 0.8229 (mtpp) REVERT: D 673 LEU cc_start: 0.8006 (tt) cc_final: 0.7742 (tp) REVERT: D 785 LYS cc_start: 0.7774 (tttt) cc_final: 0.7549 (mtmm) REVERT: D 1154 LYS cc_start: 0.8633 (tttt) cc_final: 0.8281 (ttmm) REVERT: G 45 ILE cc_start: 0.7259 (mt) cc_final: 0.7005 (mt) REVERT: G 122 GLN cc_start: 0.5801 (tm-30) cc_final: 0.4507 (mp10) REVERT: L 11 LEU cc_start: 0.5389 (mt) cc_final: 0.4956 (pt) REVERT: L 23 LEU cc_start: 0.6304 (mt) cc_final: 0.6030 (tp) outliers start: 23 outliers final: 21 residues processed: 420 average time/residue: 0.3573 time to fit residues: 246.0770 Evaluate side-chains 338 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 317 time to evaluate : 3.248 ------------------------------------------------------------------------------- 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: 0.1980 chunk 238 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 317 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 301 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS ** 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 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27533 Z= 0.210 Angle : 0.615 11.860 37981 Z= 0.327 Chirality : 0.043 0.177 4512 Planarity : 0.004 0.063 4572 Dihedral : 19.331 179.691 4957 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.74 % Favored : 91.23 % Rotamer: Outliers : 0.93 % Allowed : 3.76 % Favored : 95.31 % 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: -2.45 (0.14), residues: 3376 helix: -0.27 (0.15), residues: 1227 sheet: -1.91 (0.28), residues: 287 loop : -2.64 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 105 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE G 121 TYR 0.017 0.002 TYR C 76 ARG 0.005 0.000 ARG F 358 *********************** 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 462 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 441 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9535 (m) cc_final: 0.9308 (p) REVERT: B 80 LEU cc_start: 0.8171 (mp) cc_final: 0.7945 (mp) REVERT: B 144 ARG cc_start: 0.7516 (tpt170) cc_final: 0.7176 (ttp-170) REVERT: C 131 GLU cc_start: 0.7316 (tt0) cc_final: 0.7063 (tt0) REVERT: C 135 VAL cc_start: 0.9478 (m) cc_final: 0.9115 (m) REVERT: C 401 ILE cc_start: 0.8732 (pt) cc_final: 0.8499 (mp) REVERT: C 564 LEU cc_start: 0.9172 (tp) cc_final: 0.8752 (tp) REVERT: C 966 MET cc_start: 0.8308 (mtm) cc_final: 0.8086 (mtm) REVERT: C 1001 TRP cc_start: 0.8375 (m100) cc_final: 0.7797 (m100) REVERT: C 1074 ARG cc_start: 0.7600 (mpt-90) cc_final: 0.7010 (ttt90) REVERT: D 110 ILE cc_start: 0.7165 (mm) cc_final: 0.6856 (mm) REVERT: D 284 GLU cc_start: 0.8562 (tt0) cc_final: 0.8304 (tt0) REVERT: D 290 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7115 (tm-30) REVERT: D 329 GLN cc_start: 0.7597 (mt0) cc_final: 0.6216 (tm-30) REVERT: D 338 TYR cc_start: 0.9173 (m-80) cc_final: 0.8811 (m-10) REVERT: D 344 ILE cc_start: 0.9667 (mp) cc_final: 0.9395 (mt) REVERT: D 455 MET cc_start: 0.8456 (ttm) cc_final: 0.8217 (ttm) REVERT: D 517 LYS cc_start: 0.8604 (mttp) cc_final: 0.8209 (mtpp) REVERT: D 1154 LYS cc_start: 0.8698 (tttt) cc_final: 0.8401 (ttmm) REVERT: E 26 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8530 (tpp-160) REVERT: G 45 ILE cc_start: 0.7133 (mt) cc_final: 0.6862 (mt) REVERT: G 122 GLN cc_start: 0.6093 (tm-30) cc_final: 0.4775 (mp10) REVERT: L 11 LEU cc_start: 0.5182 (mt) cc_final: 0.4671 (pt) REVERT: L 23 LEU cc_start: 0.6166 (mt) cc_final: 0.5892 (tp) outliers start: 21 outliers final: 20 residues processed: 459 average time/residue: 0.3995 time to fit residues: 299.2509 Evaluate side-chains 352 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 332 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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: 7.9990 chunk 190 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 250 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 232 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 478 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3273 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= 0.284 Angle : 0.662 11.727 37981 Z= 0.351 Chirality : 0.044 0.191 4512 Planarity : 0.005 0.061 4572 Dihedral : 19.332 179.970 4957 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.52 % Favored : 89.45 % Rotamer: Outliers : 0.97 % Allowed : 4.38 % Favored : 94.65 % 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: -2.42 (0.14), residues: 3376 helix: -0.21 (0.15), residues: 1235 sheet: -1.87 (0.29), residues: 276 loop : -2.66 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 19 HIS 0.005 0.001 HIS C 403 PHE 0.020 0.002 PHE C 420 TYR 0.015 0.002 TYR C 563 ARG 0.005 0.001 ARG C 264 *********************** 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 436 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 414 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9553 (m) cc_final: 0.9267 (p) REVERT: A 64 GLU cc_start: 0.7620 (pt0) cc_final: 0.6533 (pp20) REVERT: C 131 GLU cc_start: 0.7377 (tt0) cc_final: 0.7027 (tt0) REVERT: C 135 VAL cc_start: 0.9577 (m) cc_final: 0.9238 (m) REVERT: C 401 ILE cc_start: 0.8740 (pt) cc_final: 0.8485 (mp) REVERT: C 1001 TRP cc_start: 0.8399 (m100) cc_final: 0.7773 (m100) REVERT: C 1074 ARG cc_start: 0.7715 (mpt-90) cc_final: 0.7108 (ttt90) REVERT: C 1078 MET cc_start: 0.8112 (mtt) cc_final: 0.7653 (mtt) REVERT: D 284 GLU cc_start: 0.8519 (tt0) cc_final: 0.8259 (tt0) REVERT: D 329 GLN cc_start: 0.7682 (mt0) cc_final: 0.6229 (tm-30) REVERT: D 344 ILE cc_start: 0.9669 (mp) cc_final: 0.9381 (mt) REVERT: D 517 LYS cc_start: 0.8605 (mttp) cc_final: 0.8303 (mtpp) REVERT: D 794 THR cc_start: 0.8622 (p) cc_final: 0.8112 (t) REVERT: D 837 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6396 (mm-30) REVERT: D 1154 LYS cc_start: 0.8732 (tttt) cc_final: 0.8419 (ttmm) REVERT: E 26 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8597 (tpp-160) REVERT: G 45 ILE cc_start: 0.7131 (mt) cc_final: 0.6816 (mt) REVERT: G 122 GLN cc_start: 0.6026 (tm-30) cc_final: 0.4677 (mp10) REVERT: L 11 LEU cc_start: 0.5394 (mt) cc_final: 0.4811 (pt) outliers start: 22 outliers final: 22 residues processed: 433 average time/residue: 0.3605 time to fit residues: 254.9345 Evaluate side-chains 351 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 329 time to evaluate : 2.838 ------------------------------------------------------------------------------- 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: 1.9990 chunk 302 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 336 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS C 287 ASN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 809 GLN F 214 HIS ** 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: 0.7591 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27533 Z= 0.172 Angle : 0.596 12.266 37981 Z= 0.313 Chirality : 0.042 0.188 4512 Planarity : 0.004 0.056 4572 Dihedral : 19.191 179.505 4957 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.55 % Favored : 92.42 % Rotamer: Outliers : 0.93 % Allowed : 2.65 % Favored : 96.42 % 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: -2.05 (0.14), residues: 3376 helix: 0.12 (0.15), residues: 1222 sheet: -1.57 (0.30), residues: 274 loop : -2.45 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 19 HIS 0.006 0.001 HIS F 214 PHE 0.017 0.001 PHE L 24 TYR 0.015 0.001 TYR D 650 ARG 0.009 0.000 ARG D 803 *********************** 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 446 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 425 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8319 (m-40) cc_final: 0.8035 (t0) REVERT: B 80 LEU cc_start: 0.8162 (mp) cc_final: 0.7929 (mp) REVERT: B 144 ARG cc_start: 0.7538 (tpt170) cc_final: 0.7116 (ttp-170) REVERT: C 131 GLU cc_start: 0.7315 (tt0) cc_final: 0.6984 (tt0) REVERT: C 188 ARG cc_start: 0.7123 (ptt90) cc_final: 0.6867 (ptt90) REVERT: C 479 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7305 (mt-10) REVERT: C 912 TYR cc_start: 0.8641 (m-10) cc_final: 0.8023 (m-10) REVERT: C 1001 TRP cc_start: 0.8318 (m100) cc_final: 0.7674 (m100) REVERT: C 1074 ARG cc_start: 0.7486 (mpt-90) cc_final: 0.6927 (ttt90) REVERT: C 1078 MET cc_start: 0.7944 (mtt) cc_final: 0.7544 (mtt) REVERT: C 1093 GLN cc_start: 0.7837 (tt0) cc_final: 0.7608 (tt0) REVERT: D 110 ILE cc_start: 0.7111 (mm) cc_final: 0.6762 (mm) REVERT: D 344 ILE cc_start: 0.9664 (mp) cc_final: 0.9393 (mt) REVERT: D 517 LYS cc_start: 0.8559 (mttp) cc_final: 0.8211 (mtpp) REVERT: D 1154 LYS cc_start: 0.8698 (tttt) cc_final: 0.8412 (ttmm) REVERT: G 45 ILE cc_start: 0.7123 (mt) cc_final: 0.6765 (mt) REVERT: L 11 LEU cc_start: 0.5527 (mt) cc_final: 0.4927 (pt) outliers start: 21 outliers final: 21 residues processed: 443 average time/residue: 0.3524 time to fit residues: 254.0339 Evaluate side-chains 353 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 332 time to evaluate : 2.665 ------------------------------------------------------------------------------- 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: 20.0000 chunk 37 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 335 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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** C 644 GLN D 255 ASN D 330 ASN ** D 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 27533 Z= 0.395 Angle : 0.758 11.380 37981 Z= 0.401 Chirality : 0.047 0.207 4512 Planarity : 0.005 0.065 4572 Dihedral : 19.338 179.544 4957 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.61 % Favored : 88.30 % Rotamer: Outliers : 0.97 % Allowed : 3.58 % Favored : 95.45 % 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: -2.45 (0.14), residues: 3376 helix: -0.30 (0.15), residues: 1231 sheet: -1.76 (0.29), residues: 290 loop : -2.66 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 19 HIS 0.007 0.002 HIS D 419 PHE 0.036 0.002 PHE C 420 TYR 0.025 0.002 TYR C 563 ARG 0.007 0.001 ARG D 91 *********************** 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 398 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 376 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8307 (m-40) cc_final: 0.7848 (t0) REVERT: C 131 GLU cc_start: 0.7378 (tt0) cc_final: 0.7092 (tt0) REVERT: C 362 ASN cc_start: 0.7649 (p0) cc_final: 0.7431 (p0) REVERT: C 459 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8041 (mttp) REVERT: C 1001 TRP cc_start: 0.8337 (m100) cc_final: 0.7844 (m100) REVERT: C 1074 ARG cc_start: 0.7736 (mpt-90) cc_final: 0.6912 (ttt90) REVERT: C 1078 MET cc_start: 0.8292 (mtt) cc_final: 0.7938 (mtt) REVERT: D 137 THR cc_start: 0.8394 (p) cc_final: 0.8151 (p) REVERT: D 344 ILE cc_start: 0.9645 (mp) cc_final: 0.9401 (mt) REVERT: D 455 MET cc_start: 0.8375 (ttm) cc_final: 0.8073 (ttm) REVERT: D 517 LYS cc_start: 0.8664 (mttp) cc_final: 0.8433 (mtpp) REVERT: D 766 SER cc_start: 0.8734 (t) cc_final: 0.8102 (m) REVERT: D 870 GLU cc_start: 0.6467 (tp30) cc_final: 0.6186 (tp30) REVERT: D 1154 LYS cc_start: 0.8720 (tttt) cc_final: 0.8346 (ttmm) REVERT: E 62 GLU cc_start: 0.8212 (tp30) cc_final: 0.7934 (tp30) REVERT: G 45 ILE cc_start: 0.7038 (mt) cc_final: 0.6826 (mt) REVERT: G 122 GLN cc_start: 0.6120 (tm-30) cc_final: 0.4706 (mp10) REVERT: L 11 LEU cc_start: 0.5794 (mt) cc_final: 0.5191 (pt) outliers start: 22 outliers final: 22 residues processed: 395 average time/residue: 0.3472 time to fit residues: 224.8828 Evaluate side-chains 314 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 292 time to evaluate : 2.753 ------------------------------------------------------------------------------- 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: 0.0040 chunk 133 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 228 optimal weight: 0.0870 chunk 165 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 263 optimal weight: 40.0000 overall best weight: 0.8176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 915 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 478 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** 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: 0.7605 moved from start: 0.4042 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= 0.167 Angle : 0.600 9.765 37981 Z= 0.315 Chirality : 0.042 0.237 4512 Planarity : 0.004 0.067 4572 Dihedral : 19.126 178.732 4957 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 0.93 % Allowed : 1.50 % Favored : 97.57 % 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: -1.98 (0.14), residues: 3376 helix: 0.14 (0.15), residues: 1234 sheet: -1.44 (0.30), residues: 281 loop : -2.43 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 19 HIS 0.004 0.001 HIS A 126 PHE 0.022 0.001 PHE D 216 TYR 0.015 0.001 TYR D 698 ARG 0.005 0.000 ARG D 802 *********************** 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 433 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 412 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8369 (m-40) cc_final: 0.8062 (t0) REVERT: B 80 LEU cc_start: 0.8110 (mp) cc_final: 0.7905 (mp) REVERT: B 144 ARG cc_start: 0.7499 (tpt170) cc_final: 0.7088 (ttp-170) REVERT: C 131 GLU cc_start: 0.7186 (tt0) cc_final: 0.6967 (tt0) REVERT: C 241 ARG cc_start: 0.4791 (mtp85) cc_final: 0.4434 (ttm170) REVERT: C 362 ASN cc_start: 0.7438 (p0) cc_final: 0.7114 (p0) REVERT: C 459 LYS cc_start: 0.8495 (mmmt) cc_final: 0.7936 (mttp) REVERT: C 912 TYR cc_start: 0.8653 (m-10) cc_final: 0.8061 (m-10) REVERT: C 1001 TRP cc_start: 0.8258 (m100) cc_final: 0.7634 (m100) REVERT: C 1074 ARG cc_start: 0.7515 (mpt-90) cc_final: 0.6893 (ttt90) REVERT: C 1078 MET cc_start: 0.8036 (mtt) cc_final: 0.7450 (mtt) REVERT: D 125 LEU cc_start: 0.7862 (mt) cc_final: 0.7574 (mt) REVERT: D 344 ILE cc_start: 0.9647 (mp) cc_final: 0.9345 (mt) REVERT: D 455 MET cc_start: 0.8517 (ttm) cc_final: 0.8139 (ttm) REVERT: D 517 LYS cc_start: 0.8589 (mttp) cc_final: 0.8304 (mtpp) REVERT: D 870 GLU cc_start: 0.6303 (tp30) cc_final: 0.6057 (tp30) REVERT: D 1154 LYS cc_start: 0.8670 (tttt) cc_final: 0.8377 (ttmm) REVERT: E 62 GLU cc_start: 0.8104 (tp30) cc_final: 0.7865 (tp30) REVERT: H 36 LYS cc_start: 0.8773 (tppt) cc_final: 0.8294 (tptt) REVERT: L 59 TYR cc_start: 0.7926 (t80) cc_final: 0.6942 (t80) outliers start: 21 outliers final: 21 residues processed: 430 average time/residue: 0.3674 time to fit residues: 257.7378 Evaluate side-chains 333 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 312 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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: 0.0270 chunk 321 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 312 optimal weight: 7.9990 chunk 188 optimal weight: 0.0030 chunk 136 optimal weight: 0.9980 chunk 245 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 282 optimal weight: 0.5980 chunk 295 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 overall best weight: 0.5248 ------------------------------------------------------------------------------- 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 D 255 ASN D 478 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 27533 Z= 0.168 Angle : 0.588 13.263 37981 Z= 0.305 Chirality : 0.041 0.168 4512 Planarity : 0.004 0.112 4572 Dihedral : 18.967 179.890 4957 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.97 % Allowed : 0.93 % Favored : 98.10 % 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 (0.15), residues: 3376 helix: 0.34 (0.15), residues: 1225 sheet: -1.19 (0.32), residues: 275 loop : -2.25 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C1081 HIS 0.007 0.001 HIS C 403 PHE 0.026 0.001 PHE H 6 TYR 0.013 0.001 TYR D 698 ARG 0.004 0.000 ARG D1072 *********************** 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 436 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 414 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 REVERT: A 222 ASN cc_start: 0.8383 (m-40) cc_final: 0.8067 (t0) REVERT: B 144 ARG cc_start: 0.7489 (tpt170) cc_final: 0.7065 (ttp-170) REVERT: C 131 GLU cc_start: 0.7212 (tt0) cc_final: 0.7000 (tt0) REVERT: C 241 ARG cc_start: 0.4244 (mtp85) cc_final: 0.3975 (ttm170) REVERT: C 362 ASN cc_start: 0.7361 (p0) cc_final: 0.7132 (p0) REVERT: C 479 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7158 (mt-10) REVERT: C 912 TYR cc_start: 0.8597 (m-10) cc_final: 0.7999 (m-10) REVERT: C 1001 TRP cc_start: 0.8215 (m100) cc_final: 0.7514 (m100) REVERT: C 1074 ARG cc_start: 0.7478 (mpt-90) cc_final: 0.6882 (ttt90) REVERT: C 1078 MET cc_start: 0.7794 (mtt) cc_final: 0.7274 (mtt) REVERT: D 125 LEU cc_start: 0.7863 (mt) cc_final: 0.7614 (mt) REVERT: D 126 GLU cc_start: 0.7856 (tp30) cc_final: 0.7329 (tp30) REVERT: D 344 ILE cc_start: 0.9634 (mp) cc_final: 0.9312 (mt) REVERT: D 455 MET cc_start: 0.8420 (ttm) cc_final: 0.8036 (ttm) REVERT: D 1154 LYS cc_start: 0.8644 (tttt) cc_final: 0.8379 (ttmm) REVERT: F 270 ILE cc_start: 0.8650 (mm) cc_final: 0.8411 (mm) REVERT: H 36 LYS cc_start: 0.8856 (tppt) cc_final: 0.8318 (tptt) REVERT: G 79 LEU cc_start: 0.7058 (tp) cc_final: 0.6762 (tp) REVERT: L 22 GLU cc_start: 0.3708 (mm-30) cc_final: 0.3464 (mm-30) outliers start: 22 outliers final: 22 residues processed: 433 average time/residue: 0.3477 time to fit residues: 250.4822 Evaluate side-chains 342 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 320 time to evaluate : 2.827 ------------------------------------------------------------------------------- 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: 8.9990 chunk 330 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 213 optimal weight: 0.0980 chunk 169 optimal weight: 4.9990 overall best weight: 2.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 330 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4326 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= 0.236 Angle : 0.629 13.120 37981 Z= 0.328 Chirality : 0.043 0.274 4512 Planarity : 0.004 0.062 4572 Dihedral : 18.983 179.447 4957 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.03 % Favored : 90.94 % Rotamer: Outliers : 0.93 % Allowed : 0.97 % Favored : 98.10 % 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: -1.76 (0.14), residues: 3376 helix: 0.32 (0.15), residues: 1228 sheet: -1.21 (0.32), residues: 273 loop : -2.30 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C1081 HIS 0.013 0.001 HIS B 220 PHE 0.020 0.002 PHE D 216 TYR 0.025 0.002 TYR C 237 ARG 0.006 0.000 ARG C 895 ********************** 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 394 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 373 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8264 (m-40) cc_final: 0.8047 (t0) REVERT: B 80 LEU cc_start: 0.8100 (mp) cc_final: 0.7869 (mp) REVERT: C 131 GLU cc_start: 0.7325 (tt0) cc_final: 0.6991 (tt0) REVERT: C 459 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7836 (mttp) REVERT: C 912 TYR cc_start: 0.8689 (m-10) cc_final: 0.8065 (m-10) REVERT: C 1001 TRP cc_start: 0.8244 (m100) cc_final: 0.7574 (m100) REVERT: C 1074 ARG cc_start: 0.7521 (mpt-90) cc_final: 0.6912 (ttt90) REVERT: C 1078 MET cc_start: 0.8123 (mtt) cc_final: 0.7549 (mtt) REVERT: D 126 GLU cc_start: 0.7937 (tp30) cc_final: 0.7512 (tp30) REVERT: D 129 ILE cc_start: 0.8435 (mm) cc_final: 0.8211 (mm) REVERT: D 255 ASN cc_start: 0.8719 (m-40) cc_final: 0.8459 (m-40) REVERT: D 344 ILE cc_start: 0.9634 (mp) cc_final: 0.9374 (mt) REVERT: D 455 MET cc_start: 0.8435 (ttm) cc_final: 0.8175 (ttm) REVERT: D 1154 LYS cc_start: 0.8682 (tttt) cc_final: 0.8277 (ttmm) REVERT: H 36 LYS cc_start: 0.8833 (tppt) cc_final: 0.8320 (tptt) REVERT: G 24 ASP cc_start: 0.5389 (t0) cc_final: 0.5093 (t0) REVERT: L 22 GLU cc_start: 0.4079 (mm-30) cc_final: 0.3638 (mm-30) outliers start: 21 outliers final: 21 residues processed: 391 average time/residue: 0.3278 time to fit residues: 214.7265 Evaluate side-chains 326 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 305 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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: 0.9990 chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 254 optimal weight: 50.0000 chunk 40 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133282 restraints weight = 52213.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132029 restraints weight = 86503.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132564 restraints weight = 80875.260| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4442 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= 0.194 Angle : 0.610 12.931 37981 Z= 0.316 Chirality : 0.042 0.179 4512 Planarity : 0.004 0.055 4572 Dihedral : 18.939 178.850 4957 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.97 % Allowed : 0.93 % Favored : 98.10 % 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: -1.73 (0.15), residues: 3376 helix: 0.32 (0.15), residues: 1233 sheet: -1.28 (0.32), residues: 284 loop : -2.25 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C1081 HIS 0.005 0.001 HIS C 403 PHE 0.020 0.001 PHE D 216 TYR 0.026 0.001 TYR C 237 ARG 0.011 0.000 ARG H 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5374.88 seconds wall clock time: 98 minutes 1.06 seconds (5881.06 seconds total)