Starting phenix.real_space_refine on Tue Apr 16 09:28:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hts_3954/04_2024/6hts_3954_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hts_3954/04_2024/6hts_3954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hts_3954/04_2024/6hts_3954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hts_3954/04_2024/6hts_3954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hts_3954/04_2024/6hts_3954_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hts_3954/04_2024/6hts_3954_updated.pdb" } resolution = 4.8 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 External origin is not on a grid point...ignoring external origin ***Please contact the Phenix developers if you need Phenix to use this external_origin*** ------------------------------------------------------------------------------- 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= 0.002 sd= 0.011 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 312 5.49 5 S 127 5.16 5 C 23263 2.51 5 N 7024 2.21 5 O 8017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E ASP 439": "OD1" <-> "OD2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 216": "OD1" <-> "OD2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 353": "NH1" <-> "NH2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F ARG 428": "NH1" <-> "NH2" Residue "G ARG 846": "NH1" <-> "NH2" Residue "G ARG 859": "NH1" <-> "NH2" Residue "G PHE 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 912": "NH1" <-> "NH2" Residue "G ARG 945": "NH1" <-> "NH2" Residue "G PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1029": "NH1" <-> "NH2" Residue "G GLU 1032": "OE1" <-> "OE2" Residue "G ARG 1035": "NH1" <-> "NH2" Residue "G ARG 1036": "NH1" <-> "NH2" Residue "G PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1089": "NH1" <-> "NH2" Residue "I TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 90": "OD1" <-> "OD2" Residue "L PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 90": "OD1" <-> "OD2" Residue "P PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 319": "NH1" <-> "NH2" Residue "R ARG 336": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38744 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3344 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3299 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3358 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 420} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3347 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3403 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3365 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 4100 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 404} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1548 Unresolved non-hydrogen angles: 1970 Unresolved non-hydrogen dihedrals: 1304 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 31, 'ARG:plan': 37, 'TYR:plan': 16, 'ASN:plan1': 20, 'TRP:plan': 9, 'ASP:plan': 21, 'PHE:plan': 17, 'GLU:plan': 23, 'HIS:plan': 11} Unresolved non-hydrogen planarities: 874 Chain: "H" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 1612 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 284} Link IDs: {'PTRANS': 15, 'TRANS': 310} Chain breaks: 3 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1086 Unresolved non-hydrogen angles: 1397 Unresolved non-hydrogen dihedrals: 920 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 9, 'TYR:plan': 18, 'ASN:plan1': 15, 'TRP:plan': 5, 'ASP:plan': 14, 'PHE:plan': 12, 'GLU:plan': 28, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 645 Chain: "I" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "J" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "N" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "O" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "P" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Chain: "R" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 533 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 12, 'TRANS': 59} Chain: "X" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "Y" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32172 SG CYS R 309 15.196 57.020 139.538 1.00491.05 S ATOM 32202 SG CYS R 314 14.803 58.094 142.961 1.00363.48 S ATOM 32327 SG CYS R 330 18.181 58.617 142.084 1.00347.03 S ATOM 32356 SG CYS R 334 16.126 54.758 142.936 1.00472.04 S Time building chain proxies: 19.55, per 1000 atoms: 0.50 Number of scatterers: 38744 At special positions: 0 Unit cell: (141.7, 179.85, 211.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 127 16.00 P 312 15.00 O 8017 8.00 N 7024 7.00 C 23263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.12 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 401 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 334 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 330 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 309 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 314 " Number of angles added : 6 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8278 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 183 helices and 27 sheets defined 44.2% alpha, 11.8% beta 124 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 17.21 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 174 through 182 Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.178A pdb=" N THR A 211 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.773A pdb=" N ASN A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.742A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.784A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 388 through 400 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.802A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.543A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.675A pdb=" N ALA A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.136A pdb=" N ASN B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.603A pdb=" N LYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 399 through 416 removed outlier: 3.752A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.975A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.783A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.219A pdb=" N THR C 211 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 273 through 289 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.997A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.582A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 381 removed outlier: 3.798A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.755A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.832A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 93 removed outlier: 3.578A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 257 through 262 removed outlier: 4.442A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 286 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.623A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 364 through 377 removed outlier: 3.677A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 396 removed outlier: 3.525A pdb=" N TYR D 387 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 388 " --> pdb=" O ASP D 385 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 389 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU D 390 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 396 " --> pdb=" O ILE D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 415 Processing helix chain 'D' and resid 423 through 432 Processing helix chain 'D' and resid 436 through 445 Processing helix chain 'E' and resid 43 through 58 removed outlier: 3.604A pdb=" N GLU E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 removed outlier: 3.786A pdb=" N ALA E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.635A pdb=" N GLN E 181 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 211 removed outlier: 4.185A pdb=" N THR E 211 " --> pdb=" O THR E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 248 Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 273 through 289 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 309 through 319 removed outlier: 3.871A pdb=" N HIS E 316 " --> pdb=" O PHE E 312 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 368 through 382 Processing helix chain 'E' and resid 388 through 400 Processing helix chain 'E' and resid 403 through 420 removed outlier: 4.057A pdb=" N LEU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Proline residue: E 412 - end of helix Processing helix chain 'E' and resid 427 through 436 Processing helix chain 'E' and resid 440 through 449 removed outlier: 3.636A pdb=" N ALA E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 65 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 176 through 184 removed outlier: 3.566A pdb=" N LEU F 182 " --> pdb=" O MET F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 212 No H-bonds generated for 'chain 'F' and resid 209 through 212' Processing helix chain 'F' and resid 244 through 252 removed outlier: 3.839A pdb=" N ASP F 248 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 249 " --> pdb=" O HIS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 262 Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 306 through 317 removed outlier: 4.047A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 351 No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 364 through 378 removed outlier: 3.738A pdb=" N LYS F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 377 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 396 Processing helix chain 'F' and resid 399 through 416 removed outlier: 3.817A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 436 through 445 Processing helix chain 'G' and resid 520 through 534 Processing helix chain 'G' and resid 545 through 547 No H-bonds generated for 'chain 'G' and resid 545 through 547' Processing helix chain 'G' and resid 549 through 558 Processing helix chain 'G' and resid 579 through 589 Processing helix chain 'G' and resid 602 through 612 Processing helix chain 'G' and resid 631 through 636 Processing helix chain 'G' and resid 638 through 643 removed outlier: 4.134A pdb=" N ARG G 643 " --> pdb=" O LYS G 639 " (cutoff:3.500A) Processing helix chain 'G' and resid 654 through 657 Processing helix chain 'G' and resid 663 through 670 Processing helix chain 'G' and resid 688 through 698 removed outlier: 3.742A pdb=" N ILE G 698 " --> pdb=" O LEU G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 728 through 740 removed outlier: 3.549A pdb=" N MET G 737 " --> pdb=" O SER G 733 " (cutoff:3.500A) Processing helix chain 'G' and resid 769 through 778 Processing helix chain 'G' and resid 809 through 815 removed outlier: 3.576A pdb=" N LYS G 814 " --> pdb=" O GLN G 811 " (cutoff:3.500A) Processing helix chain 'G' and resid 842 through 846 Processing helix chain 'G' and resid 855 through 863 Processing helix chain 'G' and resid 869 through 877 Processing helix chain 'G' and resid 889 through 893 removed outlier: 3.812A pdb=" N PHE G 893 " --> pdb=" O SER G 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 889 through 893' Processing helix chain 'G' and resid 898 through 907 Processing helix chain 'G' and resid 909 through 930 removed outlier: 4.030A pdb=" N LYS G 921 " --> pdb=" O PHE G 917 " (cutoff:3.500A) Processing helix chain 'G' and resid 938 through 941 No H-bonds generated for 'chain 'G' and resid 938 through 941' Processing helix chain 'G' and resid 959 through 964 Processing helix chain 'G' and resid 966 through 971 Processing helix chain 'G' and resid 1030 through 1039 Processing helix chain 'G' and resid 1044 through 1051 Processing helix chain 'G' and resid 1055 through 1064 Processing helix chain 'G' and resid 1101 through 1116 removed outlier: 3.828A pdb=" N SER G1115 " --> pdb=" O THR G1111 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN G1116 " --> pdb=" O ARG G1112 " (cutoff:3.500A) Processing helix chain 'G' and resid 1127 through 1138 Processing helix chain 'G' and resid 1153 through 1163 removed outlier: 3.683A pdb=" N PHE G1163 " --> pdb=" O MET G1159 " (cutoff:3.500A) Processing helix chain 'G' and resid 1176 through 1179 No H-bonds generated for 'chain 'G' and resid 1176 through 1179' Processing helix chain 'G' and resid 1202 through 1208 Processing helix chain 'G' and resid 1231 through 1247 Processing helix chain 'H' and resid 106 through 120 Processing helix chain 'H' and resid 142 through 154 Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 215 through 229 Processing helix chain 'H' and resid 231 through 236 removed outlier: 4.083A pdb=" N ALA H 235 " --> pdb=" O PRO H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 248 Processing helix chain 'H' and resid 256 through 263 Processing helix chain 'H' and resid 447 through 454 Proline residue: H 452 - end of helix Processing helix chain 'H' and resid 458 through 460 No H-bonds generated for 'chain 'H' and resid 458 through 460' Processing helix chain 'H' and resid 468 through 478 removed outlier: 3.850A pdb=" N ARG H 478 " --> pdb=" O TYR H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 483 through 489 Processing helix chain 'H' and resid 496 through 498 No H-bonds generated for 'chain 'H' and resid 496 through 498' Processing helix chain 'H' and resid 503 through 514 Processing helix chain 'H' and resid 532 through 542 Processing helix chain 'H' and resid 544 through 550 Processing helix chain 'H' and resid 554 through 560 Processing helix chain 'H' and resid 563 through 566 No H-bonds generated for 'chain 'H' and resid 563 through 566' Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 64 through 78 removed outlier: 3.663A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 113 Processing helix chain 'I' and resid 121 through 131 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 50 through 75 removed outlier: 3.619A pdb=" N ARG J 67 " --> pdb=" O GLU J 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 Processing helix chain 'K' and resid 17 through 20 No H-bonds generated for 'chain 'K' and resid 17 through 20' Processing helix chain 'K' and resid 27 through 36 Processing helix chain 'K' and resid 47 through 72 Processing helix chain 'K' and resid 80 through 89 Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'K' and resid 113 through 115 No H-bonds generated for 'chain 'K' and resid 113 through 115' Processing helix chain 'L' and resid 37 through 48 Processing helix chain 'L' and resid 56 through 84 removed outlier: 3.723A pdb=" N ASN L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 101 Processing helix chain 'L' and resid 104 through 123 Processing helix chain 'M' and resid 45 through 56 Processing helix chain 'M' and resid 64 through 78 Processing helix chain 'M' and resid 86 through 113 Processing helix chain 'M' and resid 121 through 131 Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 31 through 40 Processing helix chain 'N' and resid 50 through 75 removed outlier: 3.616A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 Processing helix chain 'O' and resid 17 through 20 No H-bonds generated for 'chain 'O' and resid 17 through 20' Processing helix chain 'O' and resid 27 through 36 Processing helix chain 'O' and resid 47 through 72 Processing helix chain 'O' and resid 80 through 89 Processing helix chain 'O' and resid 91 through 96 Processing helix chain 'O' and resid 113 through 115 No H-bonds generated for 'chain 'O' and resid 113 through 115' Processing helix chain 'P' and resid 37 through 48 Processing helix chain 'P' and resid 56 through 84 removed outlier: 3.723A pdb=" N ASN P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 101 Processing helix chain 'P' and resid 104 through 123 Processing helix chain 'R' and resid 332 through 341 removed outlier: 3.599A pdb=" N ILE R 337 " --> pdb=" O GLN R 333 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 3.526A pdb=" N MET A 359 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 327 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU A 68 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE A 329 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 229 through 239 Processing sheet with id= C, first strand: chain 'A' and resid 130 through 135 removed outlier: 4.025A pdb=" N ASP A 189 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR A 192 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ARG A 202 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLU A 194 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 200 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 138 through 141 Processing sheet with id= E, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.603A pdb=" N LEU B 355 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 324 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE B 75 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET B 326 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLY B 77 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR B 328 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 233 through 243 removed outlier: 3.652A pdb=" N LYS B 234 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 169 through 174 removed outlier: 4.247A pdb=" N GLY B 159 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU B 144 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS B 164 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL B 142 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR B 194 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LYS B 204 " --> pdb=" O THR B 194 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP B 196 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE B 202 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.881A pdb=" N VAL C 327 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU C 68 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE C 329 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 229 through 239 Processing sheet with id= J, first strand: chain 'C' and resid 167 through 172 removed outlier: 4.128A pdb=" N GLU C 137 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS C 162 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 135 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 133 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP C 189 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR C 192 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLU C 194 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 200 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 355 through 359 removed outlier: 3.686A pdb=" N LEU D 355 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU D 324 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE D 75 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET D 326 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N GLY D 77 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 328 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 299 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 233 through 243 Processing sheet with id= M, first strand: chain 'D' and resid 169 through 174 removed outlier: 3.976A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS D 164 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL D 142 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP D 191 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR D 194 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS D 204 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP D 196 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE D 202 " --> pdb=" O ASP D 196 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 359 through 363 removed outlier: 6.646A pdb=" N VAL E 327 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU E 68 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE E 329 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY E 70 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER E 331 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 229 through 239 Processing sheet with id= P, first strand: chain 'E' and resid 130 through 133 removed outlier: 4.389A pdb=" N GLY E 133 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE E 191 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR E 192 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ARG E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLU E 194 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 200 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 156 through 162 Processing sheet with id= R, first strand: chain 'F' and resid 354 through 358 removed outlier: 7.284A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU F 324 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE F 75 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET F 326 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP F 299 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 233 through 243 Processing sheet with id= T, first strand: chain 'F' and resid 169 through 174 removed outlier: 3.804A pdb=" N GLY F 159 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS F 164 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL F 142 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP F 191 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR F 194 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS F 204 " --> pdb=" O THR F 194 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 539 through 541 removed outlier: 4.192A pdb=" N GLY G 539 " --> pdb=" O ARG G 676 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU G 678 " --> pdb=" O GLY G 539 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 571 " --> pdb=" O TYR G 648 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G 650 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP G 652 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 760 through 765 removed outlier: 6.233A pdb=" N VAL G1221 " --> pdb=" O ILE G 761 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET G 763 " --> pdb=" O VAL G1221 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG G1223 " --> pdb=" O MET G 763 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N CYS G 765 " --> pdb=" O ARG G1223 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE G1225 " --> pdb=" O CYS G 765 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 831 through 833 Processing sheet with id= X, first strand: chain 'H' and resid 59 through 62 removed outlier: 4.770A pdb=" N ASN H 37 " --> pdb=" O THR H 135 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 491 through 494 removed outlier: 7.383A pdb=" N LEU H 184 " --> pdb=" O PHE H 492 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N THR H 494 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE H 186 " --> pdb=" O THR H 494 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'R' and resid 274 through 277 Processing sheet with id= AA, first strand: chain 'R' and resid 320 through 322 1455 hydrogen bonds defined for protein. 4239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 313 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 20.43 Time building geometry restraints manager: 17.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11164 1.34 - 1.45: 6803 1.45 - 1.57: 21107 1.57 - 1.69: 618 1.69 - 1.81: 209 Bond restraints: 39901 Sorted by residual: bond pdb=" C SER P 36 " pdb=" N TYR P 37 " ideal model delta sigma weight residual 1.333 1.581 -0.247 1.56e-02 4.11e+03 2.51e+02 bond pdb=" C SER L 36 " pdb=" N TYR L 37 " ideal model delta sigma weight residual 1.333 1.581 -0.247 1.56e-02 4.11e+03 2.51e+02 bond pdb=" C THR G 682 " pdb=" N PRO G 683 " ideal model delta sigma weight residual 1.334 1.428 -0.094 2.34e-02 1.83e+03 1.62e+01 bond pdb=" C1' DA Y 29 " pdb=" N9 DA Y 29 " ideal model delta sigma weight residual 1.460 1.523 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C1' DA Y -5 " pdb=" N9 DA Y -5 " ideal model delta sigma weight residual 1.460 1.519 -0.059 2.00e-02 2.50e+03 8.82e+00 ... (remaining 39896 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.30: 2538 106.30 - 113.76: 22678 113.76 - 121.22: 20035 121.22 - 128.68: 9682 128.68 - 136.14: 383 Bond angle restraints: 55316 Sorted by residual: angle pdb=" C THR I 45 " pdb=" N VAL I 46 " pdb=" CA VAL I 46 " ideal model delta sigma weight residual 120.77 125.89 -5.12 1.31e+00 5.83e-01 1.53e+01 angle pdb=" N CYS R 314 " pdb=" CA CYS R 314 " pdb=" C CYS R 314 " ideal model delta sigma weight residual 109.81 118.39 -8.58 2.21e+00 2.05e-01 1.51e+01 angle pdb=" N PRO R 315 " pdb=" CA PRO R 315 " pdb=" C PRO R 315 " ideal model delta sigma weight residual 111.26 117.44 -6.18 1.63e+00 3.76e-01 1.44e+01 angle pdb=" C ARG H 100 " pdb=" N ASN H 101 " pdb=" CA ASN H 101 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N ILE G 727 " pdb=" CA ILE G 727 " pdb=" C ILE G 727 " ideal model delta sigma weight residual 112.80 109.46 3.34 1.15e+00 7.56e-01 8.46e+00 ... (remaining 55311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.14: 21328 25.14 - 50.28: 1619 50.28 - 75.42: 506 75.42 - 100.56: 15 100.56 - 125.70: 4 Dihedral angle restraints: 23472 sinusoidal: 10671 harmonic: 12801 Sorted by residual: dihedral pdb=" CA CYS R 314 " pdb=" C CYS R 314 " pdb=" N PRO R 315 " pdb=" CA PRO R 315 " ideal model delta harmonic sigma weight residual -180.00 -135.36 -44.64 0 5.00e+00 4.00e-02 7.97e+01 dihedral pdb=" CA GLY I 44 " pdb=" C GLY I 44 " pdb=" N THR I 45 " pdb=" CA THR I 45 " ideal model delta harmonic sigma weight residual 180.00 141.99 38.01 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.70 -125.70 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 23469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4369 0.028 - 0.056: 1422 0.056 - 0.084: 333 0.084 - 0.112: 286 0.112 - 0.141: 77 Chirality restraints: 6487 Sorted by residual: chirality pdb=" CA CYS R 314 " pdb=" N CYS R 314 " pdb=" C CYS R 314 " pdb=" CB CYS R 314 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA PRO R 315 " pdb=" N PRO R 315 " pdb=" C PRO R 315 " pdb=" CB PRO R 315 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE G1090 " pdb=" N ILE G1090 " pdb=" C ILE G1090 " pdb=" CB ILE G1090 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 6484 not shown) Planarity restraints: 6100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 314 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO R 315 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 315 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 315 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G1071 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO G1072 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G1072 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G1072 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO B 99 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.024 5.00e-02 4.00e+02 ... (remaining 6097 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 132 2.44 - 3.05: 23303 3.05 - 3.67: 59284 3.67 - 4.28: 88120 4.28 - 4.90: 136991 Nonbonded interactions: 307830 Sorted by model distance: nonbonded pdb=" N2 DG X -45 " pdb=" C2 DA Y 46 " model vdw 1.820 3.420 nonbonded pdb=" C2 DG X 2 " pdb=" N2 DG Y -1 " model vdw 1.975 3.340 nonbonded pdb=" C2 DG X -51 " pdb=" N2 DG Y 52 " model vdw 2.005 3.340 nonbonded pdb=" C2 DG X 38 " pdb=" N2 DG Y -37 " model vdw 2.084 3.340 nonbonded pdb=" C2' DC Y 37 " pdb=" C7 DT Y 38 " model vdw 2.095 3.860 ... (remaining 307825 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 12 through 141 or (resid 152 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 454 or resid 501)) selection = (chain 'C' and (resid 12 through 141 or resid 152 through 454 or resid 501)) selection = (chain 'E' and (resid 12 through 141 or (resid 152 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 454 or resid 501)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 15 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 156 through 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 through 214 or resid 219 through 453 \ or resid 501)) selection = (chain 'F' and (resid 15 through 149 or resid 156 through 210 or (resid 211 thro \ ugh 214 and (name N or name CA or name C or name O or name CB )) or resid 219 or \ (resid 220 through 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 453 or resid 501)) } ncs_group { reference = chain 'I' selection = (chain 'M' and resid 40 through 135) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'K' and resid 14 through 118) selection = chain 'O' } ncs_group { reference = (chain 'L' and resid 31 through 124) selection = chain 'P' } 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=0.01 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.480 Check model and map are aligned: 0.540 Set scattering table: 0.350 Process input model: 120.180 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 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 : 0.004 0.247 39901 Z= 0.220 Angle : 0.545 8.579 55316 Z= 0.334 Chirality : 0.037 0.141 6487 Planarity : 0.003 0.052 6100 Dihedral : 17.812 125.696 15194 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.71 % Favored : 98.27 % Rotamer: Outliers : 1.39 % Allowed : 3.47 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % 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: -2.23 (0.10), residues: 4393 helix: -2.10 (0.08), residues: 2121 sheet: -0.11 (0.17), residues: 608 loop : -0.83 (0.12), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 913 HIS 0.002 0.000 HIS A 241 PHE 0.010 0.001 PHE N 100 TYR 0.008 0.001 TYR B 442 ARG 0.003 0.000 ARG G 859 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 753 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: A 278 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8710 (tm-30) REVERT: A 306 MET cc_start: 0.8130 (mtp) cc_final: 0.7896 (ttm) REVERT: A 359 MET cc_start: 0.9099 (mtm) cc_final: 0.8844 (mmt) REVERT: A 441 LYS cc_start: 0.9494 (mttt) cc_final: 0.9210 (mmmt) REVERT: B 73 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.9023 (p) REVERT: B 251 ASN cc_start: 0.7262 (m-40) cc_final: 0.6556 (m-40) REVERT: B 305 ASP cc_start: 0.9126 (t0) cc_final: 0.8849 (p0) REVERT: B 356 ILE cc_start: 0.9527 (mt) cc_final: 0.9243 (mm) REVERT: C 61 MET cc_start: 0.8309 (mmt) cc_final: 0.7976 (tpp) REVERT: C 264 MET cc_start: 0.8851 (mmm) cc_final: 0.8557 (mmm) REVERT: C 306 MET cc_start: 0.9565 (tpp) cc_final: 0.9252 (tpp) REVERT: C 313 THR cc_start: 0.9650 (m) cc_final: 0.9405 (m) REVERT: C 354 LEU cc_start: 0.9662 (tp) cc_final: 0.9436 (mt) REVERT: D 26 SER cc_start: 0.9381 (t) cc_final: 0.9126 (p) REVERT: D 123 PHE cc_start: 0.9258 (m-10) cc_final: 0.9035 (m-80) REVERT: D 185 ASP cc_start: 0.8510 (m-30) cc_final: 0.8190 (m-30) REVERT: D 193 ILE cc_start: 0.9522 (pt) cc_final: 0.9138 (mm) REVERT: D 308 SER cc_start: 0.9161 (m) cc_final: 0.8959 (p) REVERT: E 49 CYS cc_start: 0.9675 (m) cc_final: 0.9406 (p) REVERT: E 191 ILE cc_start: 0.9214 (pt) cc_final: 0.8967 (pt) REVERT: F 46 MET cc_start: 0.8139 (mmm) cc_final: 0.7772 (mpp) REVERT: F 239 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8378 (p) REVERT: F 246 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9120 (mm-30) REVERT: F 443 MET cc_start: 0.8626 (ttp) cc_final: 0.8023 (tpt) REVERT: G 888 PHE cc_start: 0.8980 (m-80) cc_final: 0.8733 (m-10) REVERT: G 905 MET cc_start: 0.8020 (tpp) cc_final: 0.7664 (tpp) REVERT: G 971 LEU cc_start: 0.9483 (tp) cc_final: 0.9231 (mt) REVERT: G 1038 LEU cc_start: 0.9034 (mt) cc_final: 0.8770 (pp) REVERT: K 24 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7751 (tm-30) REVERT: K 49 VAL cc_start: 0.5979 (t) cc_final: 0.5657 (t) REVERT: K 99 ARG cc_start: 0.7343 (mmt180) cc_final: 0.6420 (mpt180) REVERT: L 61 ILE cc_start: 0.8284 (mt) cc_final: 0.7756 (mt) REVERT: L 106 LEU cc_start: 0.7585 (mt) cc_final: 0.7227 (mt) REVERT: M 59 GLU cc_start: 0.4997 (OUTLIER) cc_final: 0.4541 (pm20) REVERT: M 67 PHE cc_start: 0.6390 (t80) cc_final: 0.6141 (t80) REVERT: P 98 VAL cc_start: 0.8536 (t) cc_final: 0.8018 (t) outliers start: 43 outliers final: 8 residues processed: 789 average time/residue: 0.5882 time to fit residues: 721.1950 Evaluate side-chains 443 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 431 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 0.5980 chunk 353 optimal weight: 50.0000 chunk 196 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 424 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 115 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 247 ASN A 380 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 78 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 240 HIS B 302 HIS B 329 ASN C 34 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS C 380 GLN C 393 HIS D 233 GLN E 42 GLN E 115 ASN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 245 HIS F 302 HIS F 344 HIS F 404 GLN G 855 HIS ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN L 82 HIS L 95 GLN ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN O 112 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS R 338 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39901 Z= 0.220 Angle : 0.582 8.087 55316 Z= 0.312 Chirality : 0.039 0.158 6487 Planarity : 0.004 0.075 6100 Dihedral : 22.346 127.605 8099 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.09 % Favored : 98.88 % Rotamer: Outliers : 0.13 % Allowed : 2.63 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 4393 helix: 0.09 (0.11), residues: 2135 sheet: 0.36 (0.17), residues: 624 loop : -0.32 (0.13), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 932 HIS 0.010 0.001 HIS C 156 PHE 0.021 0.002 PHE A 177 TYR 0.028 0.002 TYR P 37 ARG 0.015 0.001 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 470 time to evaluate : 4.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9251 (mtp180) cc_final: 0.9008 (ttp80) REVERT: A 278 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8803 (tm-30) REVERT: A 359 MET cc_start: 0.8842 (mtm) cc_final: 0.8534 (mmt) REVERT: B 15 ASP cc_start: 0.8145 (m-30) cc_final: 0.7834 (t0) REVERT: B 305 ASP cc_start: 0.9132 (t0) cc_final: 0.8918 (p0) REVERT: B 319 ASP cc_start: 0.8789 (p0) cc_final: 0.8559 (p0) REVERT: B 356 ILE cc_start: 0.9517 (mt) cc_final: 0.9283 (mp) REVERT: B 428 ARG cc_start: 0.9725 (tpt170) cc_final: 0.9470 (tpm170) REVERT: C 303 GLU cc_start: 0.9781 (mm-30) cc_final: 0.9425 (pt0) REVERT: C 306 MET cc_start: 0.9629 (tpp) cc_final: 0.9307 (tpp) REVERT: D 303 MET cc_start: 0.8045 (ppp) cc_final: 0.7683 (ttm) REVERT: D 443 MET cc_start: 0.8964 (ptm) cc_final: 0.8481 (ptm) REVERT: E 87 LEU cc_start: 0.8685 (mm) cc_final: 0.8410 (mt) REVERT: E 147 MET cc_start: 0.6890 (ptp) cc_final: 0.6123 (pmm) REVERT: E 203 GLN cc_start: 0.9495 (tt0) cc_final: 0.9224 (mt0) REVERT: F 174 LEU cc_start: 0.8206 (pt) cc_final: 0.7977 (pt) REVERT: F 246 GLU cc_start: 0.9619 (mt-10) cc_final: 0.9355 (mm-30) REVERT: F 443 MET cc_start: 0.8928 (ttp) cc_final: 0.8383 (tpt) REVERT: G 971 LEU cc_start: 0.9473 (tp) cc_final: 0.9230 (mt) REVERT: K 24 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7647 (tm-30) REVERT: K 99 ARG cc_start: 0.7437 (mmt180) cc_final: 0.5974 (mpt180) REVERT: P 45 LEU cc_start: 0.3624 (tt) cc_final: 0.3252 (tt) REVERT: P 73 ILE cc_start: 0.7346 (mt) cc_final: 0.6962 (mt) REVERT: P 80 LEU cc_start: 0.7409 (mt) cc_final: 0.6579 (mt) REVERT: R 324 ARG cc_start: 0.9732 (ttm-80) cc_final: 0.9386 (ttp-170) outliers start: 4 outliers final: 0 residues processed: 474 average time/residue: 0.5765 time to fit residues: 432.3127 Evaluate side-chains 334 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 4.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 352 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 424 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 chunk 378 optimal weight: 8.9990 chunk 421 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 340 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS D 41 GLN E 18 HIS E 280 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS G 847 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 ASN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN O 94 ASN P 47 GLN R 338 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 39901 Z= 0.332 Angle : 0.721 12.003 55316 Z= 0.384 Chirality : 0.042 0.203 6487 Planarity : 0.006 0.092 6100 Dihedral : 22.800 115.366 8099 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 0.23 % Allowed : 3.60 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 4393 helix: 0.36 (0.11), residues: 2113 sheet: 0.33 (0.18), residues: 642 loop : -0.18 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 283 HIS 0.010 0.002 HIS A 229 PHE 0.030 0.003 PHE A 437 TYR 0.030 0.002 TYR D 387 ARG 0.012 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 374 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8793 (ttp) cc_final: 0.8344 (ptm) REVERT: A 329 PHE cc_start: 0.9215 (m-10) cc_final: 0.8968 (m-80) REVERT: A 353 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8598 (p0) REVERT: A 359 MET cc_start: 0.8609 (mtm) cc_final: 0.8377 (mmt) REVERT: B 15 ASP cc_start: 0.8215 (m-30) cc_final: 0.7880 (t0) REVERT: B 319 ASP cc_start: 0.8727 (p0) cc_final: 0.8492 (p0) REVERT: C 191 ILE cc_start: 0.9534 (pt) cc_final: 0.9162 (mm) REVERT: C 303 GLU cc_start: 0.9732 (mm-30) cc_final: 0.9444 (pt0) REVERT: C 306 MET cc_start: 0.9455 (tpp) cc_final: 0.9106 (tpp) REVERT: C 332 ASN cc_start: 0.9194 (p0) cc_final: 0.8921 (p0) REVERT: D 46 MET cc_start: 0.7730 (tpt) cc_final: 0.7391 (tpt) REVERT: D 88 MET cc_start: 0.9270 (mmp) cc_final: 0.9062 (mmm) REVERT: D 443 MET cc_start: 0.9395 (ptm) cc_final: 0.9005 (ptm) REVERT: E 147 MET cc_start: 0.7533 (ptp) cc_final: 0.6563 (pmm) REVERT: E 359 MET cc_start: 0.9027 (mpp) cc_final: 0.8826 (mpp) REVERT: E 364 MET cc_start: 0.9619 (pmm) cc_final: 0.9406 (pmm) REVERT: F 90 MET cc_start: 0.9267 (ttt) cc_final: 0.9051 (tpt) REVERT: F 179 ILE cc_start: 0.8655 (mt) cc_final: 0.8452 (mm) REVERT: F 443 MET cc_start: 0.8945 (ttp) cc_final: 0.8573 (tpt) REVERT: G 835 LEU cc_start: 0.7345 (mp) cc_final: 0.6872 (mp) REVERT: G 971 LEU cc_start: 0.9516 (tp) cc_final: 0.9281 (mm) REVERT: G 1010 LEU cc_start: 0.9678 (mp) cc_final: 0.9470 (pp) REVERT: K 24 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7577 (tm-30) REVERT: P 80 LEU cc_start: 0.8284 (mt) cc_final: 0.7624 (mt) outliers start: 7 outliers final: 3 residues processed: 380 average time/residue: 0.5684 time to fit residues: 346.2929 Evaluate side-chains 280 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 20.0000 chunk 319 optimal weight: 50.0000 chunk 220 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 426 optimal weight: 0.8980 chunk 451 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS P 49 HIS R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39901 Z= 0.212 Angle : 0.573 8.569 55316 Z= 0.307 Chirality : 0.039 0.188 6487 Planarity : 0.004 0.067 6100 Dihedral : 22.635 122.472 8099 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 4393 helix: 0.85 (0.11), residues: 2123 sheet: 0.31 (0.18), residues: 652 loop : -0.09 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 913 HIS 0.008 0.001 HIS L 109 PHE 0.023 0.002 PHE G 867 TYR 0.029 0.002 TYR M 54 ARG 0.007 0.001 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8463 (ttp) cc_final: 0.7765 (ttp) REVERT: A 268 LYS cc_start: 0.8270 (tppt) cc_final: 0.8065 (ptpp) REVERT: A 329 PHE cc_start: 0.9137 (m-10) cc_final: 0.8852 (m-80) REVERT: A 359 MET cc_start: 0.8645 (mtm) cc_final: 0.8406 (mmt) REVERT: B 15 ASP cc_start: 0.8363 (m-30) cc_final: 0.8036 (t0) REVERT: B 103 ILE cc_start: 0.8398 (tp) cc_final: 0.8141 (tp) REVERT: B 442 TYR cc_start: 0.9591 (m-80) cc_final: 0.9369 (m-10) REVERT: C 191 ILE cc_start: 0.9592 (pt) cc_final: 0.9227 (mm) REVERT: C 259 MET cc_start: 0.9165 (mmm) cc_final: 0.8836 (tpt) REVERT: C 260 MET cc_start: 0.9538 (mtm) cc_final: 0.9317 (tpt) REVERT: C 264 MET cc_start: 0.8706 (mmp) cc_final: 0.8453 (mmm) REVERT: C 303 GLU cc_start: 0.9730 (mm-30) cc_final: 0.9387 (pt0) REVERT: C 306 MET cc_start: 0.9487 (tpp) cc_final: 0.9074 (tpp) REVERT: C 332 ASN cc_start: 0.9181 (p0) cc_final: 0.8874 (p0) REVERT: D 88 MET cc_start: 0.9311 (mmp) cc_final: 0.9080 (mmp) REVERT: D 443 MET cc_start: 0.9368 (ptm) cc_final: 0.9071 (ptm) REVERT: D 446 TYR cc_start: 0.9085 (m-80) cc_final: 0.8878 (m-80) REVERT: F 90 MET cc_start: 0.9255 (ttt) cc_final: 0.9011 (tpt) REVERT: F 174 LEU cc_start: 0.8610 (pt) cc_final: 0.8279 (pt) REVERT: F 197 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8843 (tptp) REVERT: F 443 MET cc_start: 0.8930 (ttp) cc_final: 0.8516 (tpt) REVERT: G 971 LEU cc_start: 0.9515 (tp) cc_final: 0.9240 (mp) REVERT: G 1010 LEU cc_start: 0.9653 (mp) cc_final: 0.9414 (pp) REVERT: K 24 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7558 (tm-30) REVERT: M 120 MET cc_start: -0.4574 (mmt) cc_final: -0.4804 (mmt) REVERT: P 80 LEU cc_start: 0.8170 (mt) cc_final: 0.7563 (mt) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.5367 time to fit residues: 322.3779 Evaluate side-chains 273 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 336 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 385 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 230 optimal weight: 20.0000 chunk 405 optimal weight: 50.0000 chunk 113 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 369 GLN ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 HIS ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS O 38 ASN O 68 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39901 Z= 0.263 Angle : 0.624 10.673 55316 Z= 0.336 Chirality : 0.040 0.163 6487 Planarity : 0.005 0.072 6100 Dihedral : 22.759 124.043 8099 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 4393 helix: 0.75 (0.11), residues: 2154 sheet: 0.25 (0.19), residues: 641 loop : -0.26 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 913 HIS 0.012 0.002 HIS B 344 PHE 0.029 0.002 PHE G 867 TYR 0.020 0.002 TYR M 99 ARG 0.015 0.001 ARG P 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8430 (ttp) cc_final: 0.7774 (ttp) REVERT: A 359 MET cc_start: 0.8466 (mtm) cc_final: 0.8177 (tpt) REVERT: B 15 ASP cc_start: 0.8318 (m-30) cc_final: 0.7975 (t0) REVERT: C 191 ILE cc_start: 0.9628 (pt) cc_final: 0.9252 (mm) REVERT: C 264 MET cc_start: 0.8657 (mmp) cc_final: 0.8454 (mmm) REVERT: C 303 GLU cc_start: 0.9747 (mm-30) cc_final: 0.9394 (pt0) REVERT: C 306 MET cc_start: 0.9530 (tpp) cc_final: 0.9201 (tpp) REVERT: C 332 ASN cc_start: 0.8993 (p0) cc_final: 0.8585 (p0) REVERT: D 443 MET cc_start: 0.9455 (ptm) cc_final: 0.9194 (ptm) REVERT: D 446 TYR cc_start: 0.9097 (m-80) cc_final: 0.8868 (m-80) REVERT: E 201 LYS cc_start: 0.8487 (tmmt) cc_final: 0.7818 (tttm) REVERT: F 197 LYS cc_start: 0.9287 (ttpt) cc_final: 0.8946 (tptp) REVERT: F 303 MET cc_start: 0.7235 (ppp) cc_final: 0.6786 (ppp) REVERT: F 443 MET cc_start: 0.8917 (ttp) cc_final: 0.8477 (tpp) REVERT: G 938 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9373 (pm20) REVERT: G 971 LEU cc_start: 0.9479 (tp) cc_final: 0.9220 (mp) REVERT: M 120 MET cc_start: -0.4057 (mmt) cc_final: -0.4277 (mmt) REVERT: P 80 LEU cc_start: 0.7965 (mt) cc_final: 0.6518 (mt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.5563 time to fit residues: 307.2196 Evaluate side-chains 256 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 0.0470 chunk 406 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 265 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 451 optimal weight: 20.0000 chunk 375 optimal weight: 30.0000 chunk 209 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 280 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 245 HIS ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN E 42 GLN E 280 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 344 HIS ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39901 Z= 0.167 Angle : 0.546 8.203 55316 Z= 0.290 Chirality : 0.038 0.171 6487 Planarity : 0.004 0.063 6100 Dihedral : 22.570 123.967 8099 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4393 helix: 1.17 (0.11), residues: 2148 sheet: 0.50 (0.19), residues: 638 loop : -0.12 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 913 HIS 0.009 0.001 HIS A 229 PHE 0.029 0.001 PHE M 104 TYR 0.021 0.001 TYR P 83 ARG 0.005 0.000 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8315 (ttp) cc_final: 0.7707 (ttp) REVERT: A 359 MET cc_start: 0.8552 (mtm) cc_final: 0.8222 (mmt) REVERT: B 15 ASP cc_start: 0.8478 (m-30) cc_final: 0.8193 (t70) REVERT: B 63 ILE cc_start: 0.8052 (mt) cc_final: 0.7792 (mt) REVERT: C 61 MET cc_start: 0.9133 (tpt) cc_final: 0.8859 (tpp) REVERT: C 191 ILE cc_start: 0.9594 (pt) cc_final: 0.9166 (mm) REVERT: C 303 GLU cc_start: 0.9735 (mm-30) cc_final: 0.9260 (pt0) REVERT: C 306 MET cc_start: 0.9478 (tpp) cc_final: 0.8996 (mmt) REVERT: C 332 ASN cc_start: 0.9134 (p0) cc_final: 0.8744 (p0) REVERT: D 88 MET cc_start: 0.9204 (mmm) cc_final: 0.8795 (mtt) REVERT: D 446 TYR cc_start: 0.9062 (m-80) cc_final: 0.8837 (m-80) REVERT: F 90 MET cc_start: 0.9458 (ttt) cc_final: 0.9244 (tpt) REVERT: F 174 LEU cc_start: 0.8529 (pt) cc_final: 0.8326 (pt) REVERT: F 197 LYS cc_start: 0.9362 (ttpt) cc_final: 0.9082 (tptt) REVERT: F 443 MET cc_start: 0.8985 (ttp) cc_final: 0.8469 (tpp) REVERT: G 938 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9385 (pm20) REVERT: K 24 GLN cc_start: 0.7461 (mm-40) cc_final: 0.6981 (tm-30) REVERT: P 80 LEU cc_start: 0.7326 (mt) cc_final: 0.6137 (mt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.5412 time to fit residues: 305.5422 Evaluate side-chains 268 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 255 optimal weight: 0.7980 chunk 380 optimal weight: 30.0000 chunk 252 optimal weight: 7.9990 chunk 450 optimal weight: 30.0000 chunk 281 optimal weight: 20.0000 chunk 274 optimal weight: 50.0000 chunk 207 optimal weight: 6.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 251 ASN F 344 HIS ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS M 125 GLN N 64 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39901 Z= 0.211 Angle : 0.573 8.160 55316 Z= 0.307 Chirality : 0.039 0.301 6487 Planarity : 0.004 0.068 6100 Dihedral : 22.607 125.180 8099 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.13), residues: 4393 helix: 1.14 (0.11), residues: 2143 sheet: 0.34 (0.19), residues: 628 loop : -0.14 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP G 913 HIS 0.015 0.001 HIS L 109 PHE 0.022 0.002 PHE G 867 TYR 0.016 0.001 TYR D 172 ARG 0.005 0.001 ARG P 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8701 (ttp) cc_final: 0.8297 (ttp) REVERT: B 15 ASP cc_start: 0.8517 (m-30) cc_final: 0.8217 (t0) REVERT: C 61 MET cc_start: 0.9195 (tpt) cc_final: 0.8983 (tpp) REVERT: C 191 ILE cc_start: 0.9569 (pt) cc_final: 0.9199 (mm) REVERT: C 286 TYR cc_start: 0.9622 (m-80) cc_final: 0.9386 (m-80) REVERT: D 88 MET cc_start: 0.9215 (mmm) cc_final: 0.8773 (mtt) REVERT: D 443 MET cc_start: 0.9444 (ptm) cc_final: 0.9113 (ptm) REVERT: F 90 MET cc_start: 0.9482 (ttt) cc_final: 0.9261 (tpt) REVERT: F 174 LEU cc_start: 0.8584 (pt) cc_final: 0.8207 (pt) REVERT: F 197 LYS cc_start: 0.9378 (ttpt) cc_final: 0.9072 (tptp) REVERT: F 443 MET cc_start: 0.9009 (ttp) cc_final: 0.8575 (tpp) REVERT: G 938 GLU cc_start: 0.9643 (mm-30) cc_final: 0.9409 (pm20) REVERT: P 45 LEU cc_start: 0.2790 (tt) cc_final: 0.2234 (tt) REVERT: P 80 LEU cc_start: 0.7652 (mt) cc_final: 0.6365 (mt) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.5420 time to fit residues: 286.9081 Evaluate side-chains 253 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 50.0000 chunk 179 optimal weight: 0.9980 chunk 268 optimal weight: 20.0000 chunk 135 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 353 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS N 64 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39901 Z= 0.187 Angle : 0.562 7.221 55316 Z= 0.299 Chirality : 0.039 0.222 6487 Planarity : 0.004 0.062 6100 Dihedral : 22.550 124.687 8099 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 4393 helix: 1.26 (0.12), residues: 2146 sheet: 0.29 (0.19), residues: 656 loop : -0.13 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP G 913 HIS 0.010 0.001 HIS L 109 PHE 0.027 0.001 PHE D 123 TYR 0.037 0.001 TYR P 83 ARG 0.005 0.000 ARG O 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 4.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8395 (ttp) cc_final: 0.7896 (ttp) REVERT: B 15 ASP cc_start: 0.8530 (m-30) cc_final: 0.8290 (t70) REVERT: C 191 ILE cc_start: 0.9566 (pt) cc_final: 0.9183 (mm) REVERT: C 247 ASN cc_start: 0.8662 (m-40) cc_final: 0.8273 (m110) REVERT: C 286 TYR cc_start: 0.9633 (m-80) cc_final: 0.9387 (m-80) REVERT: C 312 PHE cc_start: 0.9396 (m-10) cc_final: 0.9175 (m-80) REVERT: D 88 MET cc_start: 0.9232 (mmm) cc_final: 0.8826 (mtt) REVERT: D 443 MET cc_start: 0.9449 (ptm) cc_final: 0.9183 (ptm) REVERT: F 90 MET cc_start: 0.9530 (ttt) cc_final: 0.9310 (tpt) REVERT: F 197 LYS cc_start: 0.9366 (ttpt) cc_final: 0.9069 (tptp) REVERT: F 443 MET cc_start: 0.9016 (ttp) cc_final: 0.8551 (tpp) REVERT: G 938 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9406 (pm20) REVERT: P 59 MET cc_start: -0.3580 (mtm) cc_final: -0.3881 (mtt) REVERT: P 80 LEU cc_start: 0.7344 (mt) cc_final: 0.5925 (mt) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.5253 time to fit residues: 273.0092 Evaluate side-chains 257 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 4.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 393 optimal weight: 6.9990 chunk 419 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 379 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 417 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 344 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS N 64 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.8149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39901 Z= 0.230 Angle : 0.601 9.262 55316 Z= 0.321 Chirality : 0.039 0.205 6487 Planarity : 0.004 0.067 6100 Dihedral : 22.666 124.016 8099 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4393 helix: 1.13 (0.11), residues: 2135 sheet: 0.18 (0.19), residues: 655 loop : -0.26 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP G 913 HIS 0.014 0.001 HIS A 229 PHE 0.028 0.002 PHE G 867 TYR 0.034 0.002 TYR P 83 ARG 0.007 0.001 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8422 (ttp) cc_final: 0.7952 (ttp) REVERT: A 359 MET cc_start: 0.8443 (mtm) cc_final: 0.8084 (tpt) REVERT: B 15 ASP cc_start: 0.8615 (m-30) cc_final: 0.8314 (t70) REVERT: C 191 ILE cc_start: 0.9573 (pt) cc_final: 0.9180 (mm) REVERT: C 247 ASN cc_start: 0.8818 (m-40) cc_final: 0.8443 (m110) REVERT: D 88 MET cc_start: 0.9258 (mmm) cc_final: 0.8840 (mtt) REVERT: D 443 MET cc_start: 0.9462 (ptm) cc_final: 0.9171 (ptm) REVERT: E 61 MET cc_start: 0.8857 (mmm) cc_final: 0.8466 (tpt) REVERT: E 147 MET cc_start: 0.8567 (mpp) cc_final: 0.8229 (mpp) REVERT: F 90 MET cc_start: 0.9560 (ttt) cc_final: 0.9341 (tpt) REVERT: F 197 LYS cc_start: 0.9440 (ttpt) cc_final: 0.9196 (tptp) REVERT: F 443 MET cc_start: 0.9023 (ttp) cc_final: 0.8626 (tpp) REVERT: G 938 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9438 (pm20) REVERT: L 79 ARG cc_start: 0.6799 (mtm180) cc_final: 0.6557 (mtm180) REVERT: M 92 LEU cc_start: 0.6548 (mt) cc_final: 0.6299 (mt) REVERT: P 80 LEU cc_start: 0.7680 (mt) cc_final: 0.6301 (mt) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.5338 time to fit residues: 275.6910 Evaluate side-chains 250 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 50.0000 chunk 443 optimal weight: 30.0000 chunk 270 optimal weight: 50.0000 chunk 210 optimal weight: 6.9990 chunk 308 optimal weight: 0.9980 chunk 465 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 chunk 370 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 286 optimal weight: 0.0370 chunk 227 optimal weight: 20.0000 overall best weight: 4.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 344 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 ASN ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.8303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39901 Z= 0.193 Angle : 0.575 8.163 55316 Z= 0.305 Chirality : 0.039 0.198 6487 Planarity : 0.004 0.060 6100 Dihedral : 22.615 122.207 8099 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.13), residues: 4393 helix: 1.23 (0.11), residues: 2143 sheet: 0.17 (0.19), residues: 681 loop : -0.26 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 913 HIS 0.010 0.001 HIS A 229 PHE 0.030 0.002 PHE D 123 TYR 0.027 0.001 TYR M 54 ARG 0.008 0.001 ARG E 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8324 (ttp) cc_final: 0.7837 (ttp) REVERT: A 359 MET cc_start: 0.8348 (mtm) cc_final: 0.7972 (tpt) REVERT: B 15 ASP cc_start: 0.8636 (m-30) cc_final: 0.8342 (t70) REVERT: C 89 SER cc_start: 0.8947 (t) cc_final: 0.8646 (p) REVERT: C 191 ILE cc_start: 0.9563 (pt) cc_final: 0.9170 (mm) REVERT: D 88 MET cc_start: 0.9272 (mmm) cc_final: 0.8888 (mtt) REVERT: D 443 MET cc_start: 0.9381 (ptm) cc_final: 0.9068 (ptm) REVERT: E 61 MET cc_start: 0.8902 (mmm) cc_final: 0.8483 (tpt) REVERT: E 147 MET cc_start: 0.8533 (mpp) cc_final: 0.8054 (mpp) REVERT: F 90 MET cc_start: 0.9594 (ttt) cc_final: 0.9393 (tpt) REVERT: F 174 LEU cc_start: 0.8849 (pt) cc_final: 0.8570 (pt) REVERT: G 938 GLU cc_start: 0.9675 (mm-30) cc_final: 0.9434 (pm20) REVERT: P 35 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5386 (mm-30) REVERT: P 80 LEU cc_start: 0.7578 (mt) cc_final: 0.6587 (mt) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.4447 time to fit residues: 229.3623 Evaluate side-chains 258 residues out of total 3801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 8.9990 chunk 394 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 381 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.066271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047145 restraints weight = 407485.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048118 restraints weight = 274069.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048860 restraints weight = 202134.553| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.8641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39901 Z= 0.220 Angle : 0.595 9.211 55316 Z= 0.319 Chirality : 0.039 0.185 6487 Planarity : 0.004 0.066 6100 Dihedral : 22.650 120.421 8099 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4393 helix: 1.16 (0.11), residues: 2135 sheet: 0.05 (0.19), residues: 669 loop : -0.31 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 913 HIS 0.013 0.001 HIS A 229 PHE 0.029 0.002 PHE G 867 TYR 0.044 0.002 TYR C 286 ARG 0.005 0.001 ARG C 317 Origin is already at (0, 0, 0), no shifts will be applied External origin is not on a grid point...ignoring external origin ***Please contact the Phenix developers if you need Phenix to use this external_origin*** =============================================================================== Job complete usr+sys time: 7765.45 seconds wall clock time: 167 minutes 0.36 seconds (10020.36 seconds total)