Starting phenix.real_space_refine (version: dev) on Wed Dec 14 02:12:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/12_2022/6pbf_20292_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D GLU 622": "OE1" <-> "OE2" Residue "D ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18484 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 Chain: "C" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 Chain: "D" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'O6V': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'O6V': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'O6V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.74, per 1000 atoms: 0.58 Number of scatterers: 18484 At special positions: 0 Unit cell: (131.936, 131.936, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3204 8.00 N 3140 7.00 C 12008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.86 Conformation dependent library (CDL) restraints added in 2.9 seconds 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 57.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.621A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 120 through 127 removed outlier: 4.285A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 185 removed outlier: 4.253A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.182A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.542A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 4.849A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 347 removed outlier: 4.950A pdb=" N VAL A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 383 through 407 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 423 through 445 removed outlier: 4.472A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.979A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 512 removed outlier: 3.610A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 566 removed outlier: 3.688A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 588 through 606 Processing helix chain 'B' and resid 33 through 46 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 61 through 64 No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.622A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 120 through 127 removed outlier: 4.285A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 185 removed outlier: 4.253A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.182A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.542A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.848A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 347 removed outlier: 4.950A pdb=" N VAL B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 383 through 407 Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 423 through 445 removed outlier: 4.472A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 3.979A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 512 removed outlier: 3.610A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 566 removed outlier: 3.688A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 588 through 606 Processing helix chain 'C' and resid 33 through 46 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 61 through 64 No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.622A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 120 through 127 removed outlier: 4.285A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 185 removed outlier: 4.252A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 253 through 263 removed outlier: 4.182A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.542A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 4.849A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 347 removed outlier: 4.950A pdb=" N VAL C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 383 through 407 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 423 through 445 removed outlier: 4.472A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.979A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 512 removed outlier: 3.610A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 566 removed outlier: 3.688A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 588 through 606 Processing helix chain 'D' and resid 33 through 46 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 61 through 64 No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.621A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 120 through 127 removed outlier: 4.285A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 185 removed outlier: 4.253A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 253 through 263 removed outlier: 4.182A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.542A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 4.849A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 347 removed outlier: 4.950A pdb=" N VAL D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 383 through 407 Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 423 through 445 removed outlier: 4.472A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 468 removed outlier: 3.979A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 512 removed outlier: 3.610A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 566 removed outlier: 3.688A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 Processing helix chain 'D' and resid 588 through 606 Processing sheet with id= A, first strand: chain 'A' and resid 273 through 279 Processing sheet with id= B, first strand: chain 'B' and resid 273 through 279 Processing sheet with id= C, first strand: chain 'C' and resid 273 through 279 Processing sheet with id= D, first strand: chain 'D' and resid 273 through 279 824 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5936 1.35 - 1.48: 4889 1.48 - 1.61: 7883 1.61 - 1.74: 0 1.74 - 1.87: 220 Bond restraints: 18928 Sorted by residual: bond pdb=" C07 O6V A1001 " pdb=" S08 O6V A1001 " ideal model delta sigma weight residual 1.642 1.870 -0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C07 O6V A1002 " pdb=" S08 O6V A1002 " ideal model delta sigma weight residual 1.642 1.869 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C07 O6V C1001 " pdb=" S08 O6V C1001 " ideal model delta sigma weight residual 1.642 1.869 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C07 O6V B1001 " pdb=" S08 O6V B1001 " ideal model delta sigma weight residual 1.642 1.869 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C14 O6V A1002 " pdb=" N15 O6V A1002 " ideal model delta sigma weight residual 1.685 1.475 0.210 2.00e-02 2.50e+03 1.10e+02 ... (remaining 18923 not shown) Histogram of bond angle deviations from ideal: 94.48 - 102.41: 104 102.41 - 110.34: 4280 110.34 - 118.27: 10064 118.27 - 126.20: 10988 126.20 - 134.13: 336 Bond angle restraints: 25772 Sorted by residual: angle pdb=" N VAL B 313 " pdb=" CA VAL B 313 " pdb=" C VAL B 313 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" N VAL D 313 " pdb=" CA VAL D 313 " pdb=" C VAL D 313 " ideal model delta sigma weight residual 112.96 108.12 4.84 1.00e+00 1.00e+00 2.34e+01 angle pdb=" N VAL A 313 " pdb=" CA VAL A 313 " pdb=" C VAL A 313 " ideal model delta sigma weight residual 112.96 108.15 4.81 1.00e+00 1.00e+00 2.31e+01 angle pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" C VAL C 313 " ideal model delta sigma weight residual 112.96 108.16 4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" C20 O6V B1001 " pdb=" S21 O6V B1001 " pdb=" C22 O6V B1001 " ideal model delta sigma weight residual 107.53 94.48 13.05 3.00e+00 1.11e-01 1.89e+01 ... (remaining 25767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 9770 17.72 - 35.44: 1086 35.44 - 53.16: 176 53.16 - 70.88: 36 70.88 - 88.60: 24 Dihedral angle restraints: 11092 sinusoidal: 4116 harmonic: 6976 Sorted by residual: dihedral pdb=" CA PRO B 424 " pdb=" C PRO B 424 " pdb=" N PHE B 425 " pdb=" CA PHE B 425 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PRO C 424 " pdb=" C PRO C 424 " pdb=" N PHE C 425 " pdb=" CA PHE C 425 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PRO D 424 " pdb=" C PRO D 424 " pdb=" N PHE D 425 " pdb=" CA PHE D 425 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 11089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1965 0.046 - 0.091: 736 0.091 - 0.137: 192 0.137 - 0.182: 59 0.182 - 0.228: 12 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA THR C 539 " pdb=" N THR C 539 " pdb=" C THR C 539 " pdb=" CB THR C 539 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA THR B 539 " pdb=" N THR B 539 " pdb=" C THR B 539 " pdb=" CB THR B 539 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA THR A 539 " pdb=" N THR A 539 " pdb=" C THR A 539 " pdb=" CB THR A 539 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2961 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 486 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ILE D 486 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE D 486 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE D 487 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 486 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C ILE C 486 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE C 486 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE C 487 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 486 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C ILE A 486 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 486 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 487 " -0.017 2.00e-02 2.50e+03 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5615 2.82 - 3.34: 16948 3.34 - 3.86: 30235 3.86 - 4.38: 30065 4.38 - 4.90: 52482 Nonbonded interactions: 135345 Sorted by model distance: nonbonded pdb=" NH1 ARG B 470 " pdb=" OE1 GLN B 596 " model vdw 2.300 2.520 nonbonded pdb=" NH1 ARG A 470 " pdb=" OE1 GLN A 596 " model vdw 2.301 2.520 nonbonded pdb=" NH1 ARG D 470 " pdb=" OE1 GLN D 596 " model vdw 2.301 2.520 nonbonded pdb=" NH1 ARG C 470 " pdb=" OE1 GLN C 596 " model vdw 2.302 2.520 nonbonded pdb=" OG1 THR C 514 " pdb=" OE2 GLU C 515 " model vdw 2.305 2.440 ... (remaining 135340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 29 through 637) selection = (chain 'B' and resid 29 through 637) selection = (chain 'C' and resid 29 through 637) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12008 2.51 5 N 3140 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.010 Extract box with map and model: 3.260 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.160 Process input model: 46.680 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.009 0.228 18928 Z= 0.602 Angle : 1.017 13.047 25772 Z= 0.520 Chirality : 0.053 0.228 2964 Planarity : 0.007 0.064 3252 Dihedral : 15.549 88.601 6580 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.13), residues: 2368 helix: -2.30 (0.11), residues: 1376 sheet: -2.94 (0.48), residues: 56 loop : -3.75 (0.15), residues: 936 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 627 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 629 average time/residue: 0.2890 time to fit residues: 273.1020 Evaluate side-chains 403 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 184 optimal weight: 0.0170 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 84 HIS ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS A 197 ASN A 238 HIS A 370 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS B 84 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 238 HIS B 267 GLN B 370 GLN B 509 HIS C 37 ASN C 197 ASN C 267 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 HIS D 84 HIS ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN D 267 GLN D 509 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 18928 Z= 0.265 Angle : 0.692 8.236 25772 Z= 0.350 Chirality : 0.043 0.211 2964 Planarity : 0.005 0.084 3252 Dihedral : 5.175 35.529 2596 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.16), residues: 2368 helix: -0.72 (0.13), residues: 1396 sheet: -2.39 (0.58), residues: 56 loop : -3.28 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 493 time to evaluate : 2.156 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: 5 outliers final: 0 residues processed: 497 average time/residue: 0.2504 time to fit residues: 198.1592 Evaluate side-chains 368 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS B 267 GLN B 370 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 374 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 128 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 267 GLN D 587 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 18928 Z= 0.332 Angle : 0.738 7.700 25772 Z= 0.375 Chirality : 0.045 0.192 2964 Planarity : 0.005 0.053 3252 Dihedral : 5.467 42.518 2596 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 2368 helix: -0.16 (0.14), residues: 1396 sheet: -1.76 (0.64), residues: 56 loop : -3.23 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 433 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 436 average time/residue: 0.2564 time to fit residues: 179.0698 Evaluate side-chains 335 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 334 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2116 time to fit residues: 3.2747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 238 HIS A 446 ASN A 509 HIS B 267 GLN B 370 GLN C 158 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 374 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 267 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 18928 Z= 0.155 Angle : 0.605 7.768 25772 Z= 0.295 Chirality : 0.040 0.192 2964 Planarity : 0.004 0.034 3252 Dihedral : 4.795 47.916 2596 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2368 helix: 0.40 (0.14), residues: 1400 sheet: -1.77 (0.62), residues: 56 loop : -2.93 (0.19), residues: 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 463 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 465 average time/residue: 0.2466 time to fit residues: 187.4594 Evaluate side-chains 347 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 306 GLN A 446 ASN B 370 GLN B 483 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 267 GLN D 587 GLN D 637 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 18928 Z= 0.296 Angle : 0.707 7.673 25772 Z= 0.357 Chirality : 0.044 0.198 2964 Planarity : 0.005 0.171 3252 Dihedral : 5.292 57.021 2596 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2368 helix: 0.33 (0.14), residues: 1396 sheet: -1.54 (0.66), residues: 56 loop : -2.96 (0.19), residues: 916 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.2401 time to fit residues: 168.7925 Evaluate side-chains 336 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN B 37 ASN B 84 HIS B 267 GLN B 370 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 306 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 587 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18928 Z= 0.172 Angle : 0.626 11.963 25772 Z= 0.302 Chirality : 0.040 0.204 2964 Planarity : 0.004 0.085 3252 Dihedral : 4.775 58.817 2596 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2368 helix: 0.64 (0.14), residues: 1388 sheet: -1.72 (0.64), residues: 56 loop : -2.76 (0.19), residues: 924 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 447 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.2481 time to fit residues: 181.1954 Evaluate side-chains 363 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 227 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 370 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 587 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 18928 Z= 0.160 Angle : 0.612 10.731 25772 Z= 0.296 Chirality : 0.040 0.177 2964 Planarity : 0.004 0.045 3252 Dihedral : 4.611 59.919 2596 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2368 helix: 0.75 (0.14), residues: 1396 sheet: -1.63 (0.63), residues: 56 loop : -2.63 (0.20), residues: 916 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.2335 time to fit residues: 170.2164 Evaluate side-chains 342 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 0.0770 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 446 ASN B 370 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 18928 Z= 0.147 Angle : 0.606 9.865 25772 Z= 0.289 Chirality : 0.039 0.175 2964 Planarity : 0.004 0.042 3252 Dihedral : 4.446 61.872 2596 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2368 helix: 0.84 (0.14), residues: 1400 sheet: -1.58 (0.62), residues: 56 loop : -2.51 (0.20), residues: 912 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.030 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2402 time to fit residues: 177.8168 Evaluate side-chains 346 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 166 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 370 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 267 GLN B 370 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN D 587 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 18928 Z= 0.173 Angle : 0.626 11.031 25772 Z= 0.300 Chirality : 0.040 0.201 2964 Planarity : 0.004 0.066 3252 Dihedral : 4.450 59.399 2596 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2368 helix: 1.03 (0.14), residues: 1368 sheet: -1.55 (0.63), residues: 56 loop : -2.38 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 441 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 443 average time/residue: 0.2447 time to fit residues: 177.8789 Evaluate side-chains 340 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 216 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 19 optimal weight: 0.0070 chunk 144 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 370 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 18928 Z= 0.160 Angle : 0.633 12.585 25772 Z= 0.299 Chirality : 0.040 0.238 2964 Planarity : 0.004 0.063 3252 Dihedral : 4.450 60.719 2596 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2368 helix: 1.07 (0.14), residues: 1360 sheet: -1.57 (0.63), residues: 56 loop : -2.41 (0.20), residues: 952 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 1.820 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.2512 time to fit residues: 176.9145 Evaluate side-chains 334 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.2980 chunk 172 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 10 optimal weight: 0.0000 overall best weight: 2.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 238 HIS D 587 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129324 restraints weight = 38008.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132331 restraints weight = 21482.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134356 restraints weight = 14234.702| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18928 Z= 0.195 Angle : 0.653 11.591 25772 Z= 0.311 Chirality : 0.041 0.215 2964 Planarity : 0.004 0.061 3252 Dihedral : 4.510 58.155 2596 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2368 helix: 0.87 (0.14), residues: 1384 sheet: -1.47 (0.64), residues: 56 loop : -2.39 (0.20), residues: 928 =============================================================================== Job complete usr+sys time: 3684.39 seconds wall clock time: 67 minutes 32.33 seconds (4052.33 seconds total)