Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 08:26:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tra_26084/10_2023/7tra_26084.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tra_26084/10_2023/7tra_26084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tra_26084/10_2023/7tra_26084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tra_26084/10_2023/7tra_26084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tra_26084/10_2023/7tra_26084.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tra_26084/10_2023/7tra_26084.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 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 Ni 2 6.56 5 P 112 5.49 5 S 80 5.16 5 C 21961 2.51 5 N 6004 2.21 5 O 6713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "I TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 227": "OD1" <-> "OD2" Residue "I TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 316": "OD1" <-> "OD2" Residue "J TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 316": "OD1" <-> "OD2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 227": "OD1" <-> "OD2" Residue "K PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 318": "OE1" <-> "OE2" Residue "O PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 223": "OE1" <-> "OE2" Residue "O GLU 249": "OE1" <-> "OE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q ASP 194": "OD1" <-> "OD2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ASP 29": "OD1" <-> "OD2" Residue "G TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 217": "OE1" <-> "OE2" Residue "L ASP 227": "OD1" <-> "OD2" Residue "L GLU 236": "OE1" <-> "OE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 107": "OD1" <-> "OD2" Residue "M ASP 117": "OD1" <-> "OD2" Residue "M TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 39": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 34872 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4315 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "H" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "Q" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1733 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 9, 'TRANS': 209} Chain: "R" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 890 Classifications: {'DNA': 25, 'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 11 Chain: "S" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 913 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "T" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 519 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 4 Chain: "E" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2494 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2134 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.39, per 1000 atoms: 0.50 Number of scatterers: 34872 At special positions: 0 Unit cell: (114.08, 147.56, 220.72, 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) Ni 2 28.00 S 80 16.00 P 112 15.00 O 6713 8.00 N 6004 7.00 C 21961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.06 Conformation dependent library (CDL) restraints added in 4.7 seconds 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7772 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 41 sheets defined 40.2% alpha, 9.7% beta 28 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 10.86 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 removed outlier: 3.631A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 44 through 59 removed outlier: 4.108A pdb=" N GLU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 74 through 93 Processing helix chain 'A' and resid 99 through 110 removed outlier: 4.160A pdb=" N ALA A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.667A pdb=" N THR A 120 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.814A pdb=" N ALA A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 209 removed outlier: 3.757A pdb=" N ARG A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.896A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 297 through 304 removed outlier: 4.013A pdb=" N GLU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.814A pdb=" N ARG A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 371 through 389 removed outlier: 4.833A pdb=" N ALA A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 removed outlier: 3.875A pdb=" N GLU A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.354A pdb=" N ARG A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 4.029A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 620 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 52 through 72 Processing helix chain 'B' and resid 98 through 114 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 193 through 204 removed outlier: 3.559A pdb=" N LYS B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 removed outlier: 3.512A pdb=" N ILE B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.770A pdb=" N HIS B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 removed outlier: 3.665A pdb=" N THR B 239 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 240 " --> pdb=" O LEU B 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 236 through 240' Processing helix chain 'B' and resid 265 through 278 Processing helix chain 'B' and resid 282 through 295 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 311 through 325 removed outlier: 4.235A pdb=" N PHE B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 3.980A pdb=" N VAL B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 24 through 33 removed outlier: 3.730A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 62 removed outlier: 3.698A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Proline residue: C 52 - end of helix Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.519A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 101 removed outlier: 3.860A pdb=" N LEU C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.707A pdb=" N ASN D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.855A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 62 removed outlier: 4.118A pdb=" N LEU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.526A pdb=" N GLY H 22 " --> pdb=" O GLN H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 69 removed outlier: 4.191A pdb=" N LEU H 55 " --> pdb=" O THR H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 114 Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 144 through 151 Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 227 through 248 removed outlier: 3.910A pdb=" N ILE H 243 " --> pdb=" O LEU H 239 " (cutoff:3.500A) Proline residue: H 244 - end of helix Processing helix chain 'H' and resid 286 through 298 Processing helix chain 'H' and resid 324 through 335 removed outlier: 3.926A pdb=" N MET H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.610A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 Processing helix chain 'I' and resid 107 through 114 removed outlier: 3.777A pdb=" N GLU I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 241 through 246 removed outlier: 4.360A pdb=" N MET I 245 " --> pdb=" O ALA I 241 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 246 " --> pdb=" O LEU I 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 241 through 246' Processing helix chain 'I' and resid 286 through 300 Processing helix chain 'I' and resid 324 through 335 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.608A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.890A pdb=" N LEU J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 107 through 115 Processing helix chain 'J' and resid 115 through 121 removed outlier: 3.669A pdb=" N ASP J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 152 Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 241 through 247 removed outlier: 3.735A pdb=" N MET J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 301 Processing helix chain 'J' and resid 324 through 335 removed outlier: 4.460A pdb=" N MET J 335 " --> pdb=" O ASN J 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 68 removed outlier: 3.808A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 4.129A pdb=" N ARG K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 242 through 243 No H-bonds generated for 'chain 'K' and resid 242 through 243' Processing helix chain 'K' and resid 244 through 248 removed outlier: 3.789A pdb=" N GLY K 248 " --> pdb=" O MET K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 301 Processing helix chain 'K' and resid 325 through 333 Processing helix chain 'O' and resid 30 through 46 Processing helix chain 'O' and resid 54 through 70 Processing helix chain 'O' and resid 129 through 141 removed outlier: 3.863A pdb=" N MET O 141 " --> pdb=" O LEU O 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 41 removed outlier: 5.503A pdb=" N ASN Q 27 " --> pdb=" O GLU Q 23 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) Proline residue: Q 31 - end of helix removed outlier: 3.687A pdb=" N GLY Q 41 " --> pdb=" O MET Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 59 removed outlier: 3.521A pdb=" N LEU Q 59 " --> pdb=" O THR Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 65 removed outlier: 5.921A pdb=" N GLY Q 63 " --> pdb=" O HIS Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 75 Processing helix chain 'Q' and resid 83 through 101 removed outlier: 4.287A pdb=" N VAL Q 87 " --> pdb=" O ARG Q 83 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET Q 99 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS Q 101 " --> pdb=" O LYS Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 115 removed outlier: 3.544A pdb=" N ALA Q 106 " --> pdb=" O ASP Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 128 Processing helix chain 'Q' and resid 134 through 140 removed outlier: 3.808A pdb=" N VAL Q 138 " --> pdb=" O THR Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 164 removed outlier: 3.501A pdb=" N GLU Q 153 " --> pdb=" O MET Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 191 removed outlier: 3.735A pdb=" N VAL Q 178 " --> pdb=" O THR Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 211 Proline residue: Q 208 - end of helix Processing helix chain 'Q' and resid 215 through 220 removed outlier: 3.805A pdb=" N ALA Q 219 " --> pdb=" O GLY Q 215 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA Q 220 " --> pdb=" O ALA Q 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 215 through 220' Processing helix chain 'E' and resid 5 through 16 removed outlier: 3.507A pdb=" N LEU E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 33 Processing helix chain 'E' and resid 39 through 61 Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 100 removed outlier: 3.573A pdb=" N LEU E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 25 through 33 Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.732A pdb=" N LEU F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 59 removed outlier: 3.681A pdb=" N LEU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 removed outlier: 4.568A pdb=" N GLN F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 removed outlier: 3.800A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 removed outlier: 4.471A pdb=" N ILE G 8 " --> pdb=" O TRP G 4 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 33 removed outlier: 3.894A pdb=" N ASP G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.726A pdb=" N LEU G 40 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 62 Processing helix chain 'G' and resid 70 through 82 removed outlier: 4.252A pdb=" N ILE G 74 " --> pdb=" O SER G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 100 removed outlier: 4.159A pdb=" N LEU G 90 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 68 removed outlier: 3.746A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 76 removed outlier: 3.874A pdb=" N ASN L 75 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.671A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 144 through 152 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 248 removed outlier: 3.800A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 298 removed outlier: 4.081A pdb=" N ARG L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 301 No H-bonds generated for 'chain 'L' and resid 299 through 301' Processing helix chain 'L' and resid 325 through 334 Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.736A pdb=" N LYS M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 Processing helix chain 'M' and resid 108 through 114 Processing helix chain 'M' and resid 115 through 122 Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 153 through 157 removed outlier: 3.973A pdb=" N ILE M 157 " --> pdb=" O GLU M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 Processing helix chain 'M' and resid 286 through 301 removed outlier: 3.682A pdb=" N GLY M 301 " --> pdb=" O ALA M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 336 Processing helix chain 'N' and resid 51 through 69 removed outlier: 3.527A pdb=" N LEU N 55 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 3.899A pdb=" N ARG N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'N' and resid 116 through 121 Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.608A pdb=" N ILE N 148 " --> pdb=" O THR N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 242 through 247 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.985A pdb=" N ALA N 289 " --> pdb=" O ASP N 285 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY N 301 " --> pdb=" O ALA N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 336 removed outlier: 3.709A pdb=" N VAL N 336 " --> pdb=" O LEU N 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.791A pdb=" N TYR A 70 " --> pdb=" O VAL A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 removed outlier: 7.466A pdb=" N ARG A 234 " --> pdb=" O ILE A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 175 removed outlier: 4.412A pdb=" N SER B 261 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU B 251 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 259 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 14 current: chain 'H' and resid 182 through 201 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 182 through 201 current: chain 'H' and resid 304 through 309 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 32 through 37 Processing sheet with id=AB1, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 125 removed outlier: 6.715A pdb=" N PHE H 123 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG H 131 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA H 125 " --> pdb=" O GLY H 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 14 current: chain 'I' and resid 185 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 185 through 201 current: chain 'I' and resid 305 through 309 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 31 through 33 Processing sheet with id=AB5, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AB6, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'J' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 2 through 14 current: chain 'J' and resid 186 through 201 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 186 through 201 current: chain 'J' and resid 305 through 309 Processing sheet with id=AB8, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AB9, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AC1, first strand: chain 'J' and resid 123 through 124 removed outlier: 3.589A pdb=" N PHE J 123 " --> pdb=" O ARG J 132 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG J 132 " --> pdb=" O PHE J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 26 through 29 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 26 through 29 current: chain 'K' and resid 183 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 183 through 201 current: chain 'K' and resid 305 through 309 removed outlier: 6.772A pdb=" N VAL K 306 " --> pdb=" O THR K 320 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL K 322 " --> pdb=" O VAL K 306 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR K 308 " --> pdb=" O VAL K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AC4, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'K' and resid 123 through 125 Processing sheet with id=AC6, first strand: chain 'O' and resid 77 through 80 removed outlier: 3.534A pdb=" N LEU O 119 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE O 3 " --> pdb=" O PHE O 160 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE O 160 " --> pdb=" O ILE O 3 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU O 5 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA O 158 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS O 7 " --> pdb=" O VAL O 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 113 through 115 Processing sheet with id=AC8, first strand: chain 'O' and resid 90 through 94 Processing sheet with id=AC9, first strand: chain 'O' and resid 168 through 169 removed outlier: 3.621A pdb=" N ALA O 168 " --> pdb=" O VAL O 240 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL O 240 " --> pdb=" O ALA O 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'O' and resid 174 through 175 Processing sheet with id=AD2, first strand: chain 'O' and resid 244 through 246 Processing sheet with id=AD3, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 306 through 309 Processing sheet with id=AD4, first strand: chain 'L' and resid 26 through 27 removed outlier: 3.501A pdb=" N ILE L 160 " --> pdb=" O ARG L 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AD6, first strand: chain 'L' and resid 95 through 96 Processing sheet with id=AD7, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 185 through 201 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 185 through 201 current: chain 'M' and resid 305 through 309 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AE1, first strand: chain 'M' and resid 123 through 124 Processing sheet with id=AE2, first strand: chain 'N' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 10 current: chain 'N' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 193 through 201 current: chain 'N' and resid 305 through 309 removed outlier: 6.707A pdb=" N VAL N 306 " --> pdb=" O THR N 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'N' and resid 32 through 35 Processing sheet with id=AE4, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AE5, first strand: chain 'N' and resid 123 through 125 1124 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 11.14 Time building geometry restraints manager: 15.98 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: 10779 1.34 - 1.46: 6238 1.46 - 1.58: 18407 1.58 - 1.70: 219 1.70 - 1.82: 144 Bond restraints: 35787 Sorted by residual: bond pdb=" CB PRO Q 119 " pdb=" CG PRO Q 119 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" N ALA A 611 " pdb=" CA ALA A 611 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.32e-02 5.74e+03 2.93e+00 bond pdb=" CG PRO Q 119 " pdb=" CD PRO Q 119 " ideal model delta sigma weight residual 1.503 1.546 -0.043 3.40e-02 8.65e+02 1.57e+00 bond pdb=" CG GLU G 78 " pdb=" CD GLU G 78 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.48e+00 bond pdb=" CG LEU Q 128 " pdb=" CD1 LEU Q 128 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 35782 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.95: 1001 104.95 - 112.23: 18364 112.23 - 119.50: 11751 119.50 - 126.78: 17086 126.78 - 134.06: 764 Bond angle restraints: 48966 Sorted by residual: angle pdb=" CA PRO Q 119 " pdb=" N PRO Q 119 " pdb=" CD PRO Q 119 " ideal model delta sigma weight residual 112.00 105.16 6.84 1.40e+00 5.10e-01 2.38e+01 angle pdb=" N GLU G 78 " pdb=" CA GLU G 78 " pdb=" CB GLU G 78 " ideal model delta sigma weight residual 110.07 116.21 -6.14 1.45e+00 4.76e-01 1.79e+01 angle pdb=" N ILE C 5 " pdb=" CA ILE C 5 " pdb=" C ILE C 5 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.59e+01 angle pdb=" C LEU G 77 " pdb=" N GLU G 78 " pdb=" CA GLU G 78 " ideal model delta sigma weight residual 120.44 115.43 5.01 1.36e+00 5.41e-01 1.36e+01 angle pdb=" C LEU N 242 " pdb=" N ILE N 243 " pdb=" CA ILE N 243 " ideal model delta sigma weight residual 120.33 123.09 -2.76 8.00e-01 1.56e+00 1.19e+01 ... (remaining 48961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20685 35.99 - 71.98: 511 71.98 - 107.98: 22 107.98 - 143.97: 1 143.97 - 179.96: 5 Dihedral angle restraints: 21224 sinusoidal: 9141 harmonic: 12083 Sorted by residual: dihedral pdb=" CB CYS F 63 " pdb=" SG CYS F 63 " pdb=" SG CYS F 108 " pdb=" CB CYS F 108 " ideal model delta sinusoidal sigma weight residual 93.00 -177.29 -89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" O4' U R 3 " pdb=" C1' U R 3 " pdb=" N1 U R 3 " pdb=" C2 U R 3 " ideal model delta sinusoidal sigma weight residual 200.00 42.74 157.26 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" CA THR Q 134 " pdb=" C THR Q 134 " pdb=" N PRO Q 135 " pdb=" CA PRO Q 135 " ideal model delta harmonic sigma weight residual 180.00 -142.02 -37.98 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 21221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4369 0.049 - 0.097: 988 0.097 - 0.146: 230 0.146 - 0.194: 10 0.194 - 0.243: 5 Chirality restraints: 5602 Sorted by residual: chirality pdb=" C3' U R 27 " pdb=" C4' U R 27 " pdb=" O3' U R 27 " pdb=" C2' U R 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.26 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1' U R 31 " pdb=" O4' U R 31 " pdb=" C2' U R 31 " pdb=" N1 U R 31 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO Q 119 " pdb=" N PRO Q 119 " pdb=" C PRO Q 119 " pdb=" CB PRO Q 119 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 5599 not shown) Planarity restraints: 5877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 610 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C LEU A 610 " -0.071 2.00e-02 2.50e+03 pdb=" O LEU A 610 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA A 611 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 100 " 0.026 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP F 100 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP F 100 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 100 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 100 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 100 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 100 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 100 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 118 " 0.063 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO Q 119 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Q 119 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 119 " 0.051 5.00e-02 4.00e+02 ... (remaining 5874 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 456 2.59 - 3.17: 31064 3.17 - 3.75: 59812 3.75 - 4.32: 80362 4.32 - 4.90: 129441 Nonbonded interactions: 301135 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 61 " pdb="NI NI Q 301 " model vdw 2.017 2.180 nonbonded pdb=" OH TYR E 11 " pdb=" O ALA E 47 " model vdw 2.129 2.440 nonbonded pdb=" OG SER A 203 " pdb=" OE2 GLU A 398 " model vdw 2.134 2.440 nonbonded pdb=" OD1 ASP A 219 " pdb=" N LYS A 220 " model vdw 2.138 2.520 nonbonded pdb=" O LEU A 77 " pdb=" NE2 GLN A 81 " model vdw 2.159 2.520 ... (remaining 301130 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 'C' selection = (chain 'D' and resid 3 through 109) selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'J' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and resid 1 through 335) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 7.450 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 93.420 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 : 0.003 0.092 35787 Z= 0.161 Angle : 0.605 9.873 48966 Z= 0.310 Chirality : 0.043 0.243 5602 Planarity : 0.004 0.092 5877 Dihedral : 15.235 179.961 13434 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.63 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4126 helix: 0.62 (0.14), residues: 1501 sheet: -0.58 (0.22), residues: 559 loop : -1.95 (0.13), residues: 2066 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 3.992 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 outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.4309 time to fit residues: 459.9872 Evaluate side-chains 467 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 3.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 214 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 380 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN A 406 HIS ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN H 17 ASN H 53 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 53 ASN J 229 ASN ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 ASN N 290 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35787 Z= 0.226 Angle : 0.618 11.615 48966 Z= 0.313 Chirality : 0.044 0.314 5602 Planarity : 0.004 0.049 5877 Dihedral : 14.659 178.687 5677 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.73 % Favored : 92.03 % Rotamer: Outliers : 1.60 % Allowed : 11.25 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4126 helix: 0.59 (0.14), residues: 1559 sheet: -0.54 (0.21), residues: 597 loop : -1.94 (0.14), residues: 1970 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 524 time to evaluate : 3.476 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 outliers start: 55 outliers final: 37 residues processed: 553 average time/residue: 0.4372 time to fit residues: 409.1368 Evaluate side-chains 503 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 466 time to evaluate : 3.730 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3513 time to fit residues: 28.9131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 381 optimal weight: 0.0000 chunk 411 optimal weight: 4.9990 chunk 339 optimal weight: 4.9990 chunk 378 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 305 optimal weight: 0.0070 overall best weight: 2.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN A 406 HIS ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35787 Z= 0.301 Angle : 0.656 11.866 48966 Z= 0.336 Chirality : 0.046 0.378 5602 Planarity : 0.005 0.099 5877 Dihedral : 14.732 177.524 5677 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.22 % Favored : 91.52 % Rotamer: Outliers : 1.92 % Allowed : 15.24 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4126 helix: 0.28 (0.13), residues: 1587 sheet: -0.56 (0.20), residues: 638 loop : -1.97 (0.14), residues: 1901 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 509 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 37 residues processed: 550 average time/residue: 0.4444 time to fit residues: 411.4882 Evaluate side-chains 470 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 433 time to evaluate : 3.849 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3209 time to fit residues: 27.7148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 382 optimal weight: 0.9990 chunk 405 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 362 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN A 406 HIS B 156 ASN ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN D 107 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35787 Z= 0.204 Angle : 0.623 13.430 48966 Z= 0.309 Chirality : 0.044 0.369 5602 Planarity : 0.004 0.050 5877 Dihedral : 14.672 177.588 5677 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.76 % Favored : 91.98 % Rotamer: Outliers : 1.31 % Allowed : 18.74 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 4126 helix: 0.31 (0.13), residues: 1595 sheet: -0.49 (0.20), residues: 644 loop : -1.97 (0.14), residues: 1887 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 476 time to evaluate : 4.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 501 average time/residue: 0.4283 time to fit residues: 365.1433 Evaluate side-chains 457 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 431 time to evaluate : 3.874 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3313 time to fit residues: 21.7777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 8.9990 chunk 229 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 167 optimal weight: 0.0870 chunk 345 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS B 185 GLN ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 ASN ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 HIS ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 35787 Z= 0.318 Angle : 0.682 16.358 48966 Z= 0.341 Chirality : 0.046 0.349 5602 Planarity : 0.005 0.055 5877 Dihedral : 14.754 176.719 5677 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.36 % Favored : 91.40 % Rotamer: Outliers : 2.21 % Allowed : 19.52 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 4126 helix: 0.24 (0.13), residues: 1587 sheet: -0.56 (0.20), residues: 671 loop : -2.00 (0.14), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 471 time to evaluate : 3.886 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 outliers start: 76 outliers final: 44 residues processed: 525 average time/residue: 0.4560 time to fit residues: 400.6256 Evaluate side-chains 472 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 428 time to evaluate : 4.032 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3278 time to fit residues: 32.3348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 2.9990 chunk 364 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 405 optimal weight: 0.7980 chunk 336 optimal weight: 0.0870 chunk 187 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35787 Z= 0.192 Angle : 0.638 13.950 48966 Z= 0.316 Chirality : 0.044 0.337 5602 Planarity : 0.004 0.054 5877 Dihedral : 14.767 178.242 5677 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.80 % Favored : 91.98 % Rotamer: Outliers : 1.57 % Allowed : 21.07 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4126 helix: 0.31 (0.13), residues: 1588 sheet: -0.62 (0.20), residues: 674 loop : -1.99 (0.14), residues: 1864 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 476 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 25 residues processed: 517 average time/residue: 0.4326 time to fit residues: 376.0399 Evaluate side-chains 464 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 439 time to evaluate : 3.720 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3526 time to fit residues: 20.6929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 296 optimal weight: 30.0000 chunk 229 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 403 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 246 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35787 Z= 0.281 Angle : 0.678 15.095 48966 Z= 0.339 Chirality : 0.045 0.315 5602 Planarity : 0.004 0.057 5877 Dihedral : 14.793 177.449 5677 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.53 % Favored : 91.25 % Rotamer: Outliers : 1.60 % Allowed : 21.65 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4126 helix: 0.25 (0.13), residues: 1589 sheet: -0.79 (0.21), residues: 633 loop : -1.98 (0.14), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 467 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 32 residues processed: 499 average time/residue: 0.4551 time to fit residues: 383.1513 Evaluate side-chains 449 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 417 time to evaluate : 3.577 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3398 time to fit residues: 24.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 249 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 275 optimal weight: 6.9990 chunk 199 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 317 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35787 Z= 0.276 Angle : 0.688 15.309 48966 Z= 0.343 Chirality : 0.045 0.315 5602 Planarity : 0.004 0.058 5877 Dihedral : 14.844 179.073 5677 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.36 % Favored : 91.42 % Rotamer: Outliers : 0.93 % Allowed : 23.02 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 4126 helix: 0.19 (0.13), residues: 1594 sheet: -0.66 (0.20), residues: 680 loop : -2.06 (0.14), residues: 1852 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 438 time to evaluate : 3.908 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 outliers start: 32 outliers final: 16 residues processed: 461 average time/residue: 0.4549 time to fit residues: 352.5963 Evaluate side-chains 438 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 422 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3359 time to fit residues: 15.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 367 optimal weight: 0.5980 chunk 386 optimal weight: 0.9990 chunk 352 optimal weight: 0.3980 chunk 376 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 340 optimal weight: 0.0670 chunk 355 optimal weight: 0.4980 chunk 375 optimal weight: 2.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35787 Z= 0.196 Angle : 0.681 15.009 48966 Z= 0.335 Chirality : 0.045 0.310 5602 Planarity : 0.004 0.055 5877 Dihedral : 14.838 179.990 5677 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.29 % Favored : 91.44 % Rotamer: Outliers : 0.44 % Allowed : 23.98 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 4126 helix: 0.20 (0.13), residues: 1601 sheet: -0.82 (0.21), residues: 630 loop : -2.00 (0.14), residues: 1895 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 461 time to evaluate : 3.841 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 outliers start: 15 outliers final: 9 residues processed: 470 average time/residue: 0.4696 time to fit residues: 366.9728 Evaluate side-chains 444 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 435 time to evaluate : 3.794 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3274 time to fit residues: 10.5355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 247 optimal weight: 7.9990 chunk 397 optimal weight: 0.9980 chunk 242 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 417 optimal weight: 6.9990 chunk 384 optimal weight: 6.9990 chunk 332 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35787 Z= 0.263 Angle : 0.704 15.357 48966 Z= 0.350 Chirality : 0.046 0.297 5602 Planarity : 0.004 0.058 5877 Dihedral : 14.809 177.273 5677 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.75 % Favored : 91.01 % Rotamer: Outliers : 0.44 % Allowed : 24.83 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 4126 helix: 0.20 (0.13), residues: 1591 sheet: -0.66 (0.20), residues: 679 loop : -2.04 (0.14), residues: 1856 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 436 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 443 average time/residue: 0.4572 time to fit residues: 338.1050 Evaluate side-chains 421 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 416 time to evaluate : 3.689 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3660 time to fit residues: 8.3924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 264 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 306 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 341 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.107555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084862 restraints weight = 101857.838| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.45 r_work: 0.3415 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35787 Z= 0.217 Angle : 0.705 15.425 48966 Z= 0.347 Chirality : 0.045 0.295 5602 Planarity : 0.004 0.057 5877 Dihedral : 14.847 177.724 5677 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.68 % Favored : 91.06 % Rotamer: Outliers : 0.26 % Allowed : 25.29 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 4126 helix: 0.18 (0.13), residues: 1595 sheet: -0.84 (0.21), residues: 623 loop : -1.93 (0.14), residues: 1908 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7819.26 seconds wall clock time: 143 minutes 38.34 seconds (8618.34 seconds total)