Starting phenix.real_space_refine on Sun Mar 17 17:43:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_20292_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_20292.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_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_20292/03_2024/6pbf_20292_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_20292_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_20292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_20292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_20292_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbf_20292/03_2024/6pbf_20292_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.27, per 1000 atoms: 0.56 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: 8.25 Conformation dependent library (CDL) restraints added in 3.6 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: 4.64 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: 5.57 Time building geometry restraints manager: 8.86 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 1.639 1.870 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C07 O6V A1002 " pdb=" S08 O6V A1002 " ideal model delta sigma weight residual 1.639 1.869 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C07 O6V C1001 " pdb=" S08 O6V C1001 " ideal model delta sigma weight residual 1.639 1.869 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C07 O6V B1001 " pdb=" S08 O6V B1001 " ideal model delta sigma weight residual 1.639 1.869 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C14 O6V A1002 " pdb=" N15 O6V A1002 " ideal model delta sigma weight residual 1.690 1.475 0.215 2.00e-02 2.50e+03 1.16e+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 107.58 94.48 13.10 3.00e+00 1.11e-01 1.91e+01 ... (remaining 25767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 10082 20.96 - 41.92: 870 41.92 - 62.88: 104 62.88 - 83.84: 40 83.84 - 104.80: 12 Dihedral angle restraints: 11108 sinusoidal: 4132 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 11105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1969 0.046 - 0.091: 732 0.091 - 0.137: 196 0.137 - 0.182: 55 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 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.910 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 52.610 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 0.231 18928 Z= 0.595 Angle : 1.011 13.097 25772 Z= 0.519 Chirality : 0.053 0.228 2964 Planarity : 0.007 0.064 3252 Dihedral : 15.975 104.798 6596 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 % Allowed : 9.83 % Favored : 89.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 286 HIS 0.007 0.001 HIS B 84 PHE 0.021 0.002 PHE A 244 TYR 0.016 0.002 TYR D 547 ARG 0.003 0.000 ARG B 363 *********************** 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 : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.8538 (pt) cc_final: 0.7970 (pt) REVERT: A 242 THR cc_start: 0.8656 (m) cc_final: 0.8233 (m) REVERT: A 315 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 415 TYR cc_start: 0.7063 (t80) cc_final: 0.6411 (t80) REVERT: A 436 VAL cc_start: 0.9203 (t) cc_final: 0.8914 (p) REVERT: A 547 TYR cc_start: 0.8088 (m-80) cc_final: 0.7617 (m-10) REVERT: B 83 LEU cc_start: 0.8129 (mp) cc_final: 0.7643 (tt) REVERT: B 146 ARG cc_start: 0.6698 (ttp-110) cc_final: 0.5586 (mtt90) REVERT: B 283 ILE cc_start: 0.9132 (tt) cc_final: 0.8692 (tt) REVERT: B 435 LEU cc_start: 0.7939 (tp) cc_final: 0.7581 (tp) REVERT: B 440 MET cc_start: 0.7607 (tpt) cc_final: 0.7356 (tpt) REVERT: B 523 PHE cc_start: 0.6754 (m-80) cc_final: 0.6448 (m-80) REVERT: C 105 LEU cc_start: 0.8831 (tp) cc_final: 0.8624 (tp) REVERT: C 172 CYS cc_start: 0.7753 (p) cc_final: 0.7314 (m) REVERT: C 193 ASP cc_start: 0.6181 (p0) cc_final: 0.5876 (p0) REVERT: C 202 ILE cc_start: 0.8636 (mm) cc_final: 0.8413 (mm) REVERT: C 364 ASP cc_start: 0.7318 (t0) cc_final: 0.7074 (t0) REVERT: C 440 MET cc_start: 0.6896 (tpt) cc_final: 0.6461 (tpt) REVERT: D 42 GLU cc_start: 0.8852 (tp30) cc_final: 0.8489 (tp30) REVERT: D 55 GLU cc_start: 0.8165 (tp30) cc_final: 0.7770 (pt0) REVERT: D 146 ARG cc_start: 0.8255 (ttp-110) cc_final: 0.7134 (ttm170) REVERT: D 301 LYS cc_start: 0.8767 (mttp) cc_final: 0.8551 (ttpt) REVERT: D 370 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7349 (pt0) outliers start: 4 outliers final: 0 residues processed: 629 average time/residue: 0.2979 time to fit residues: 279.6178 Evaluate side-chains 410 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 2.216 ------------------------------------------------------------------------------- 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 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7723 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18928 Z= 0.262 Angle : 0.688 8.083 25772 Z= 0.348 Chirality : 0.043 0.184 2964 Planarity : 0.005 0.072 3252 Dihedral : 7.672 102.570 2612 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.27 % Allowed : 6.28 % Favored : 93.45 % 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: -2.61 (0.16), residues: 2368 helix: -0.72 (0.13), residues: 1404 sheet: -2.38 (0.58), residues: 56 loop : -3.34 (0.17), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 286 HIS 0.009 0.001 HIS D 185 PHE 0.017 0.002 PHE A 244 TYR 0.020 0.002 TYR A 339 ARG 0.006 0.001 ARG B 615 *********************** 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 : 2.217 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: A 29 TRP cc_start: 0.6108 (p90) cc_final: 0.5654 (p90) REVERT: A 105 LEU cc_start: 0.9089 (tp) cc_final: 0.8772 (tp) REVERT: A 161 TYR cc_start: 0.7996 (t80) cc_final: 0.7720 (t80) REVERT: A 202 ILE cc_start: 0.8685 (mm) cc_final: 0.8451 (mm) REVERT: A 315 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 415 TYR cc_start: 0.7342 (t80) cc_final: 0.7044 (t80) REVERT: A 435 LEU cc_start: 0.8682 (tp) cc_final: 0.8337 (tp) REVERT: A 447 MET cc_start: 0.7447 (mmt) cc_final: 0.6945 (mmm) REVERT: A 495 TRP cc_start: 0.8694 (m100) cc_final: 0.8120 (m100) REVERT: B 128 GLN cc_start: 0.7930 (tt0) cc_final: 0.7497 (tp40) REVERT: B 146 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6043 (mmt90) REVERT: B 315 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 364 ASP cc_start: 0.7704 (t70) cc_final: 0.7487 (t0) REVERT: B 415 TYR cc_start: 0.7839 (t80) cc_final: 0.7237 (t80) REVERT: B 435 LEU cc_start: 0.8424 (tp) cc_final: 0.8039 (tp) REVERT: B 554 MET cc_start: 0.7805 (tpt) cc_final: 0.7602 (tpp) REVERT: C 197 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6789 (p0) REVERT: C 202 ILE cc_start: 0.8808 (mm) cc_final: 0.8549 (mm) REVERT: C 315 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6873 (mm-30) REVERT: C 390 LEU cc_start: 0.8941 (mt) cc_final: 0.8711 (tt) REVERT: C 432 TYR cc_start: 0.9022 (t80) cc_final: 0.8606 (t80) REVERT: C 447 MET cc_start: 0.7426 (mmm) cc_final: 0.6941 (mmm) REVERT: C 523 PHE cc_start: 0.7731 (m-10) cc_final: 0.7478 (m-80) REVERT: C 525 ASP cc_start: 0.6867 (p0) cc_final: 0.6618 (p0) REVERT: C 593 TRP cc_start: 0.8385 (t60) cc_final: 0.7789 (t60) REVERT: D 42 GLU cc_start: 0.8882 (tp30) cc_final: 0.8557 (tp30) REVERT: D 54 LYS cc_start: 0.8282 (tttm) cc_final: 0.8051 (tmtt) REVERT: D 146 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.6743 (ttm170) REVERT: D 370 GLN cc_start: 0.7571 (tp-100) cc_final: 0.7133 (pt0) REVERT: D 435 LEU cc_start: 0.8357 (tp) cc_final: 0.8035 (tt) REVERT: D 633 VAL cc_start: 0.9013 (t) cc_final: 0.8797 (m) REVERT: D 635 ASN cc_start: 0.8429 (t0) cc_final: 0.8167 (t0) outliers start: 5 outliers final: 0 residues processed: 497 average time/residue: 0.2578 time to fit residues: 202.0195 Evaluate side-chains 382 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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: 7.9990 chunk 66 optimal weight: 0.0770 chunk 178 optimal weight: 4.9990 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: 2.9990 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS B 267 GLN B 370 GLN C 158 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 158 ASN D 185 HIS D 267 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18928 Z= 0.215 Angle : 0.619 7.754 25772 Z= 0.311 Chirality : 0.041 0.224 2964 Planarity : 0.004 0.052 3252 Dihedral : 7.211 104.027 2612 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % 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: -1.79 (0.17), residues: 2368 helix: 0.02 (0.14), residues: 1404 sheet: -1.82 (0.64), residues: 56 loop : -3.15 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 462 HIS 0.003 0.001 HIS A 238 PHE 0.019 0.002 PHE D 512 TYR 0.024 0.002 TYR A 547 ARG 0.007 0.000 ARG A 632 *********************** 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 464 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6088 (p90) cc_final: 0.5760 (p90) REVERT: A 128 GLN cc_start: 0.8159 (tt0) cc_final: 0.7762 (tp40) REVERT: A 202 ILE cc_start: 0.8790 (mm) cc_final: 0.8462 (mm) REVERT: A 315 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7015 (mm-30) REVERT: A 415 TYR cc_start: 0.7594 (t80) cc_final: 0.7336 (t80) REVERT: A 442 MET cc_start: 0.7980 (tpp) cc_final: 0.7738 (tpp) REVERT: A 481 MET cc_start: 0.7972 (tpp) cc_final: 0.7586 (tpp) REVERT: A 547 TYR cc_start: 0.7997 (m-80) cc_final: 0.7578 (m-10) REVERT: A 592 LEU cc_start: 0.8811 (tp) cc_final: 0.8143 (tt) REVERT: B 146 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.6098 (mtt90) REVERT: B 364 ASP cc_start: 0.7878 (t70) cc_final: 0.7599 (t0) REVERT: B 435 LEU cc_start: 0.8937 (tp) cc_final: 0.8617 (tp) REVERT: B 522 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7184 (mm-30) REVERT: B 554 MET cc_start: 0.8056 (tpt) cc_final: 0.7806 (tpp) REVERT: B 592 LEU cc_start: 0.8914 (tp) cc_final: 0.8451 (tt) REVERT: B 608 MET cc_start: 0.7820 (tpp) cc_final: 0.7587 (tpp) REVERT: C 128 GLN cc_start: 0.8212 (tt0) cc_final: 0.7776 (tp40) REVERT: C 315 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6925 (mm-30) REVERT: C 447 MET cc_start: 0.6892 (mmm) cc_final: 0.6672 (mmm) REVERT: C 491 MET cc_start: 0.8866 (mmm) cc_final: 0.8639 (tpp) REVERT: D 42 GLU cc_start: 0.8849 (tp30) cc_final: 0.8440 (tp30) REVERT: D 54 LYS cc_start: 0.8235 (tttm) cc_final: 0.7953 (tmtt) REVERT: D 146 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.6728 (ttm110) REVERT: D 318 SER cc_start: 0.8910 (m) cc_final: 0.8679 (t) REVERT: D 633 VAL cc_start: 0.9069 (t) cc_final: 0.8840 (m) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.2513 time to fit residues: 186.2725 Evaluate side-chains 359 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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: 3.9990 chunk 161 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS B 128 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 636 HIS ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 374 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18928 Z= 0.243 Angle : 0.656 8.892 25772 Z= 0.326 Chirality : 0.043 0.248 2964 Planarity : 0.004 0.033 3252 Dihedral : 7.343 107.866 2612 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.96 % 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: -1.38 (0.17), residues: 2368 helix: 0.35 (0.14), residues: 1400 sheet: -1.54 (0.65), residues: 56 loop : -2.99 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 286 HIS 0.005 0.001 HIS D 582 PHE 0.019 0.002 PHE B 534 TYR 0.019 0.002 TYR A 547 ARG 0.004 0.000 ARG A 134 *********************** 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 450 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.9008 (tt) cc_final: 0.8802 (tt) REVERT: A 128 GLN cc_start: 0.8165 (tt0) cc_final: 0.7817 (tp40) REVERT: A 178 ILE cc_start: 0.8531 (mm) cc_final: 0.8296 (mm) REVERT: A 315 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7068 (mm-30) REVERT: A 317 VAL cc_start: 0.8754 (t) cc_final: 0.8541 (p) REVERT: A 403 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6215 (tp30) REVERT: A 432 TYR cc_start: 0.8967 (t80) cc_final: 0.8661 (t80) REVERT: A 481 MET cc_start: 0.8193 (tpp) cc_final: 0.7792 (tpp) REVERT: A 547 TYR cc_start: 0.8237 (m-80) cc_final: 0.7990 (m-10) REVERT: A 593 TRP cc_start: 0.8828 (t60) cc_final: 0.8211 (t60) REVERT: B 146 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.6215 (mtt90) REVERT: B 364 ASP cc_start: 0.7999 (t70) cc_final: 0.7667 (t0) REVERT: B 435 LEU cc_start: 0.8945 (tp) cc_final: 0.8629 (tp) REVERT: B 481 MET cc_start: 0.8201 (tpp) cc_final: 0.7823 (tpp) REVERT: B 554 MET cc_start: 0.8317 (tpt) cc_final: 0.8045 (tpp) REVERT: B 592 LEU cc_start: 0.8868 (tp) cc_final: 0.8309 (tt) REVERT: B 608 MET cc_start: 0.7952 (tpp) cc_final: 0.7740 (tpp) REVERT: C 315 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7165 (mm-30) REVERT: C 317 VAL cc_start: 0.8998 (m) cc_final: 0.8738 (p) REVERT: C 318 SER cc_start: 0.8693 (m) cc_final: 0.8258 (t) REVERT: C 389 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8343 (tp30) REVERT: D 42 GLU cc_start: 0.8856 (tp30) cc_final: 0.8357 (tp30) REVERT: D 54 LYS cc_start: 0.8156 (tttm) cc_final: 0.7803 (tmtt) REVERT: D 128 GLN cc_start: 0.7954 (tt0) cc_final: 0.7650 (tp40) REVERT: D 146 ARG cc_start: 0.8104 (ttp-110) cc_final: 0.6599 (ttm110) REVERT: D 491 MET cc_start: 0.8771 (mmm) cc_final: 0.8529 (tpp) REVERT: D 588 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7274 (mm-30) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.2421 time to fit residues: 175.5296 Evaluate side-chains 356 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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: 10.0000 chunk 129 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 0.1980 chunk 204 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 370 GLN C 84 HIS ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS C 267 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6142 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= 0.209 Angle : 0.625 7.720 25772 Z= 0.309 Chirality : 0.042 0.249 2964 Planarity : 0.004 0.046 3252 Dihedral : 7.126 103.532 2612 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: -1.06 (0.17), residues: 2368 helix: 0.58 (0.14), residues: 1396 sheet: -1.51 (0.65), residues: 56 loop : -2.77 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 286 HIS 0.004 0.001 HIS C 84 PHE 0.021 0.002 PHE A 456 TYR 0.021 0.001 TYR B 89 ARG 0.006 0.000 ARG A 134 *********************** 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 446 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.9017 (tt) cc_final: 0.8791 (tt) REVERT: A 105 LEU cc_start: 0.9389 (tp) cc_final: 0.9055 (tp) REVERT: A 128 GLN cc_start: 0.8168 (tt0) cc_final: 0.7824 (tp40) REVERT: A 178 ILE cc_start: 0.8703 (mm) cc_final: 0.8382 (mm) REVERT: A 315 GLU cc_start: 0.7644 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 317 VAL cc_start: 0.8784 (t) cc_final: 0.8581 (p) REVERT: A 403 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6176 (tp30) REVERT: A 432 TYR cc_start: 0.8968 (t80) cc_final: 0.8708 (t80) REVERT: A 435 LEU cc_start: 0.8926 (tp) cc_final: 0.8691 (tt) REVERT: A 474 MET cc_start: 0.7659 (mtm) cc_final: 0.7459 (mtp) REVERT: A 481 MET cc_start: 0.8106 (tpp) cc_final: 0.7685 (tpp) REVERT: A 570 MET cc_start: 0.7767 (tpp) cc_final: 0.7394 (tpp) REVERT: A 593 TRP cc_start: 0.8860 (t60) cc_final: 0.8248 (t60) REVERT: B 128 GLN cc_start: 0.7982 (tt0) cc_final: 0.7713 (tp40) REVERT: B 146 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.6325 (mmt90) REVERT: B 294 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7668 (tt0) REVERT: B 364 ASP cc_start: 0.8203 (t70) cc_final: 0.7908 (t0) REVERT: B 435 LEU cc_start: 0.8910 (tp) cc_final: 0.8619 (tp) REVERT: B 481 MET cc_start: 0.8237 (tpp) cc_final: 0.7801 (tpp) REVERT: B 547 TYR cc_start: 0.8699 (m-10) cc_final: 0.8270 (m-10) REVERT: B 554 MET cc_start: 0.8343 (tpt) cc_final: 0.7994 (tpp) REVERT: B 578 MET cc_start: 0.8156 (ttm) cc_final: 0.7787 (ttm) REVERT: B 592 LEU cc_start: 0.8871 (tp) cc_final: 0.8381 (tt) REVERT: C 260 MET cc_start: 0.9158 (mmt) cc_final: 0.8928 (tpp) REVERT: C 315 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7078 (mm-30) REVERT: C 317 VAL cc_start: 0.9004 (m) cc_final: 0.8709 (p) REVERT: C 318 SER cc_start: 0.8668 (m) cc_final: 0.8265 (t) REVERT: C 474 MET cc_start: 0.7886 (ttm) cc_final: 0.7534 (ttp) REVERT: C 481 MET cc_start: 0.8410 (tpp) cc_final: 0.7750 (tpp) REVERT: C 592 LEU cc_start: 0.8795 (tp) cc_final: 0.8501 (tt) REVERT: C 603 MET cc_start: 0.8383 (tpp) cc_final: 0.8183 (mmm) REVERT: D 42 GLU cc_start: 0.8822 (tp30) cc_final: 0.8282 (tp30) REVERT: D 54 LYS cc_start: 0.8114 (tttm) cc_final: 0.7722 (tmtt) REVERT: D 128 GLN cc_start: 0.7939 (tt0) cc_final: 0.7601 (tp40) REVERT: D 146 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.6586 (ttm110) REVERT: D 268 TRP cc_start: 0.8050 (p-90) cc_final: 0.7617 (p-90) REVERT: D 324 TYR cc_start: 0.7908 (m-80) cc_final: 0.7590 (m-10) REVERT: D 588 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7317 (mm-30) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.2443 time to fit residues: 175.8443 Evaluate side-chains 353 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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: 4.9990 chunk 205 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 189 optimal weight: 0.0770 chunk 105 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.5142 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18928 Z= 0.158 Angle : 0.583 8.100 25772 Z= 0.284 Chirality : 0.040 0.247 2964 Planarity : 0.003 0.036 3252 Dihedral : 6.745 99.195 2612 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.54 % 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: -0.76 (0.18), residues: 2368 helix: 0.77 (0.14), residues: 1412 sheet: -1.53 (0.64), residues: 56 loop : -2.58 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 286 HIS 0.003 0.001 HIS D 84 PHE 0.022 0.001 PHE B 534 TYR 0.031 0.001 TYR B 161 ARG 0.005 0.000 ARG A 134 *********************** 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 450 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8125 (tt0) cc_final: 0.7755 (tp40) REVERT: A 134 ARG cc_start: 0.8553 (tpp80) cc_final: 0.7975 (tpp-160) REVERT: A 178 ILE cc_start: 0.8688 (mm) cc_final: 0.8356 (mm) REVERT: A 219 LEU cc_start: 0.9015 (mm) cc_final: 0.8801 (mt) REVERT: A 315 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6901 (mm-30) REVERT: A 403 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6232 (tp30) REVERT: A 435 LEU cc_start: 0.8871 (tp) cc_final: 0.8665 (tt) REVERT: A 474 MET cc_start: 0.7536 (mtm) cc_final: 0.7285 (mtp) REVERT: A 481 MET cc_start: 0.8159 (tpp) cc_final: 0.7766 (tpp) REVERT: A 593 TRP cc_start: 0.8706 (t60) cc_final: 0.7713 (t60) REVERT: A 603 MET cc_start: 0.8552 (tpp) cc_final: 0.8255 (tpp) REVERT: A 629 TRP cc_start: 0.8343 (m-90) cc_final: 0.8090 (m-90) REVERT: B 128 GLN cc_start: 0.7974 (tt0) cc_final: 0.7618 (tp40) REVERT: B 146 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.6365 (mmt90) REVERT: B 294 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7634 (tt0) REVERT: B 364 ASP cc_start: 0.8014 (t70) cc_final: 0.7708 (t0) REVERT: B 435 LEU cc_start: 0.8886 (tp) cc_final: 0.8572 (tp) REVERT: B 481 MET cc_start: 0.8163 (tpp) cc_final: 0.7824 (tpp) REVERT: B 491 MET cc_start: 0.8852 (mmm) cc_final: 0.8365 (tpp) REVERT: B 554 MET cc_start: 0.8173 (tpt) cc_final: 0.7883 (tpp) REVERT: B 568 LEU cc_start: 0.9078 (tp) cc_final: 0.8865 (tt) REVERT: B 592 LEU cc_start: 0.8909 (tp) cc_final: 0.8328 (tt) REVERT: C 315 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7006 (mm-30) REVERT: C 317 VAL cc_start: 0.8952 (m) cc_final: 0.8697 (p) REVERT: C 474 MET cc_start: 0.7412 (ttm) cc_final: 0.7191 (ttp) REVERT: C 481 MET cc_start: 0.8401 (tpp) cc_final: 0.7795 (tpp) REVERT: C 570 MET cc_start: 0.7732 (tpp) cc_final: 0.6714 (mmm) REVERT: D 42 GLU cc_start: 0.8792 (tp30) cc_final: 0.8286 (tp30) REVERT: D 54 LYS cc_start: 0.8132 (tttm) cc_final: 0.7762 (tmtt) REVERT: D 128 GLN cc_start: 0.7838 (tt0) cc_final: 0.7540 (tp40) REVERT: D 146 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.6575 (mmt90) REVERT: D 266 VAL cc_start: 0.8929 (t) cc_final: 0.8645 (p) REVERT: D 489 ASP cc_start: 0.7536 (m-30) cc_final: 0.6781 (m-30) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.2474 time to fit residues: 178.8890 Evaluate side-chains 361 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 0.0980 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 370 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6532 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= 0.146 Angle : 0.587 10.399 25772 Z= 0.283 Chirality : 0.040 0.243 2964 Planarity : 0.003 0.036 3252 Dihedral : 6.498 97.068 2612 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -0.65 (0.18), residues: 2368 helix: 0.75 (0.14), residues: 1440 sheet: -1.45 (0.64), residues: 56 loop : -2.44 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 286 HIS 0.003 0.001 HIS B 84 PHE 0.018 0.001 PHE A 115 TYR 0.020 0.001 TYR B 161 ARG 0.004 0.000 ARG A 134 *********************** 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 451 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8701 (mmp) cc_final: 0.8399 (mmt) REVERT: A 128 GLN cc_start: 0.8056 (tt0) cc_final: 0.7675 (tp40) REVERT: A 134 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8063 (tpp-160) REVERT: A 178 ILE cc_start: 0.8642 (mm) cc_final: 0.8342 (mm) REVERT: A 315 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6896 (mm-30) REVERT: A 403 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6407 (tp30) REVERT: A 481 MET cc_start: 0.8086 (tpp) cc_final: 0.7696 (tpp) REVERT: A 593 TRP cc_start: 0.8704 (t60) cc_final: 0.8087 (t60) REVERT: A 603 MET cc_start: 0.8458 (tpp) cc_final: 0.8169 (tpp) REVERT: A 629 TRP cc_start: 0.8385 (m-90) cc_final: 0.8152 (m-90) REVERT: B 146 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.6365 (mmt90) REVERT: B 294 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7603 (tt0) REVERT: B 364 ASP cc_start: 0.7992 (t70) cc_final: 0.7728 (t0) REVERT: B 435 LEU cc_start: 0.8882 (tp) cc_final: 0.8552 (tp) REVERT: B 481 MET cc_start: 0.8041 (tpp) cc_final: 0.7705 (tpp) REVERT: B 491 MET cc_start: 0.8774 (mmm) cc_final: 0.8363 (tpp) REVERT: B 568 LEU cc_start: 0.9061 (tp) cc_final: 0.8819 (tt) REVERT: B 592 LEU cc_start: 0.8898 (tp) cc_final: 0.8455 (tt) REVERT: C 315 GLU cc_start: 0.7694 (mm-30) cc_final: 0.6745 (mm-30) REVERT: C 317 VAL cc_start: 0.8908 (m) cc_final: 0.8634 (p) REVERT: D 42 GLU cc_start: 0.8784 (tp30) cc_final: 0.8346 (tp30) REVERT: D 54 LYS cc_start: 0.8113 (tttm) cc_final: 0.7750 (tmtt) REVERT: D 128 GLN cc_start: 0.7799 (tt0) cc_final: 0.7541 (tp40) REVERT: D 146 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.6506 (mmt90) REVERT: D 246 LEU cc_start: 0.9205 (tp) cc_final: 0.8955 (tt) REVERT: D 266 VAL cc_start: 0.8877 (t) cc_final: 0.8533 (p) REVERT: D 481 MET cc_start: 0.8356 (tpp) cc_final: 0.7956 (tpp) REVERT: D 489 ASP cc_start: 0.7203 (m-30) cc_final: 0.5941 (m-30) REVERT: D 491 MET cc_start: 0.8489 (mmm) cc_final: 0.8105 (tpp) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.2399 time to fit residues: 174.5486 Evaluate side-chains 365 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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: 0.7980 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6660 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= 0.156 Angle : 0.602 12.740 25772 Z= 0.288 Chirality : 0.040 0.241 2964 Planarity : 0.003 0.047 3252 Dihedral : 6.409 95.063 2612 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -0.51 (0.18), residues: 2368 helix: 0.91 (0.14), residues: 1416 sheet: -1.47 (0.64), residues: 56 loop : -2.39 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 29 HIS 0.003 0.001 HIS D 509 PHE 0.022 0.001 PHE D 512 TYR 0.018 0.001 TYR B 161 ARG 0.004 0.000 ARG A 134 *********************** 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 456 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8748 (mmp) cc_final: 0.8476 (mmt) REVERT: A 128 GLN cc_start: 0.8072 (tt0) cc_final: 0.7675 (tp40) REVERT: A 134 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8041 (tpp-160) REVERT: A 315 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6895 (tp30) REVERT: A 481 MET cc_start: 0.8163 (tpp) cc_final: 0.7710 (tpp) REVERT: A 593 TRP cc_start: 0.8781 (t60) cc_final: 0.8173 (t60) REVERT: A 603 MET cc_start: 0.8496 (tpp) cc_final: 0.8183 (tpp) REVERT: A 629 TRP cc_start: 0.8389 (m-90) cc_final: 0.8177 (m-90) REVERT: B 128 GLN cc_start: 0.8013 (tt0) cc_final: 0.7656 (tp40) REVERT: B 146 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.6383 (mtt90) REVERT: B 294 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7602 (tt0) REVERT: B 364 ASP cc_start: 0.8001 (t70) cc_final: 0.7716 (t0) REVERT: B 435 LEU cc_start: 0.8885 (tp) cc_final: 0.8588 (tp) REVERT: B 491 MET cc_start: 0.8770 (mmm) cc_final: 0.8448 (tpp) REVERT: B 568 LEU cc_start: 0.9105 (tp) cc_final: 0.8806 (tt) REVERT: B 592 LEU cc_start: 0.8940 (tp) cc_final: 0.8459 (tt) REVERT: C 315 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6772 (mm-30) REVERT: C 317 VAL cc_start: 0.8901 (m) cc_final: 0.8591 (p) REVERT: C 318 SER cc_start: 0.8616 (m) cc_final: 0.8252 (t) REVERT: C 435 LEU cc_start: 0.8722 (tp) cc_final: 0.8368 (tt) REVERT: C 481 MET cc_start: 0.8423 (tpp) cc_final: 0.8140 (tpp) REVERT: C 501 ILE cc_start: 0.8794 (tt) cc_final: 0.8534 (tp) REVERT: D 42 GLU cc_start: 0.8746 (tp30) cc_final: 0.8313 (tp30) REVERT: D 54 LYS cc_start: 0.8088 (tttm) cc_final: 0.7730 (tmtt) REVERT: D 128 GLN cc_start: 0.7823 (tt0) cc_final: 0.7561 (tp40) REVERT: D 146 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.6495 (mmt90) REVERT: D 246 LEU cc_start: 0.9223 (tp) cc_final: 0.8957 (tt) REVERT: D 266 VAL cc_start: 0.8853 (t) cc_final: 0.8543 (p) REVERT: D 315 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7185 (mm-30) REVERT: D 481 MET cc_start: 0.8367 (tpp) cc_final: 0.8003 (tpp) REVERT: D 489 ASP cc_start: 0.7179 (m-30) cc_final: 0.6716 (m-30) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2408 time to fit residues: 177.5111 Evaluate side-chains 362 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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: 0.0980 chunk 198 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 166 optimal weight: 0.0030 chunk 65 optimal weight: 20.0000 chunk 191 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6784 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 : 0.610 11.326 25772 Z= 0.292 Chirality : 0.040 0.241 2964 Planarity : 0.003 0.036 3252 Dihedral : 6.338 94.670 2612 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.47 (0.18), residues: 2368 helix: 0.94 (0.14), residues: 1412 sheet: -1.55 (0.64), residues: 56 loop : -2.33 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 286 HIS 0.004 0.001 HIS D 509 PHE 0.021 0.001 PHE B 534 TYR 0.017 0.001 TYR B 161 ARG 0.004 0.000 ARG A 134 *********************** 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 452 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8749 (mmp) cc_final: 0.8441 (mmt) REVERT: A 128 GLN cc_start: 0.8113 (tt0) cc_final: 0.7716 (tp40) REVERT: A 134 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8132 (tpp-160) REVERT: A 178 ILE cc_start: 0.8651 (mm) cc_final: 0.8344 (mm) REVERT: A 315 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7004 (tp30) REVERT: A 403 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6571 (tp30) REVERT: A 481 MET cc_start: 0.8197 (tpp) cc_final: 0.7736 (tpp) REVERT: A 593 TRP cc_start: 0.8788 (t60) cc_final: 0.8090 (t60) REVERT: A 603 MET cc_start: 0.8478 (tpp) cc_final: 0.8131 (tpp) REVERT: B 128 GLN cc_start: 0.8019 (tt0) cc_final: 0.7665 (tp40) REVERT: B 146 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.6409 (mmt90) REVERT: B 294 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7611 (tt0) REVERT: B 364 ASP cc_start: 0.8197 (t70) cc_final: 0.7924 (t0) REVERT: B 435 LEU cc_start: 0.8913 (tp) cc_final: 0.8580 (tp) REVERT: B 481 MET cc_start: 0.8070 (tpp) cc_final: 0.7803 (tpp) REVERT: C 315 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6795 (mm-30) REVERT: C 317 VAL cc_start: 0.8898 (m) cc_final: 0.8596 (p) REVERT: C 318 SER cc_start: 0.8603 (m) cc_final: 0.8239 (t) REVERT: C 432 TYR cc_start: 0.8452 (t80) cc_final: 0.8206 (t80) REVERT: C 435 LEU cc_start: 0.8803 (tp) cc_final: 0.8429 (tt) REVERT: C 481 MET cc_start: 0.8434 (tpp) cc_final: 0.7997 (tmm) REVERT: C 497 MET cc_start: 0.8690 (ttp) cc_final: 0.8439 (ttp) REVERT: C 501 ILE cc_start: 0.8741 (tt) cc_final: 0.8480 (tp) REVERT: D 42 GLU cc_start: 0.8748 (tp30) cc_final: 0.8380 (tp30) REVERT: D 54 LYS cc_start: 0.8072 (tttm) cc_final: 0.7720 (tmtt) REVERT: D 128 GLN cc_start: 0.7831 (tt0) cc_final: 0.7563 (tp40) REVERT: D 146 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.6520 (mmt90) REVERT: D 246 LEU cc_start: 0.9224 (tp) cc_final: 0.8972 (tt) REVERT: D 315 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7227 (mm-30) REVERT: D 481 MET cc_start: 0.8361 (tpp) cc_final: 0.7999 (tpp) REVERT: D 489 ASP cc_start: 0.7102 (m-30) cc_final: 0.5965 (m-30) REVERT: D 596 GLN cc_start: 0.8508 (pt0) cc_final: 0.8129 (pt0) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2449 time to fit residues: 179.0270 Evaluate side-chains 361 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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: 6.9990 chunk 155 optimal weight: 8.9990 chunk 235 optimal weight: 0.0570 chunk 216 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 199 optimal weight: 0.7980 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18928 Z= 0.161 Angle : 0.621 11.654 25772 Z= 0.297 Chirality : 0.040 0.240 2964 Planarity : 0.003 0.045 3252 Dihedral : 6.314 94.173 2612 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -0.46 (0.18), residues: 2368 helix: 0.95 (0.14), residues: 1412 sheet: -1.55 (0.64), residues: 56 loop : -2.33 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 286 HIS 0.003 0.001 HIS D 509 PHE 0.025 0.001 PHE A 256 TYR 0.016 0.001 TYR B 161 ARG 0.004 0.000 ARG A 134 ********************** 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 444 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8073 (tt0) cc_final: 0.7699 (tp40) REVERT: A 178 ILE cc_start: 0.8660 (mm) cc_final: 0.8372 (mm) REVERT: A 315 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7002 (tp30) REVERT: A 403 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6628 (tp30) REVERT: A 481 MET cc_start: 0.8053 (tpp) cc_final: 0.7647 (tpp) REVERT: A 570 MET cc_start: 0.7696 (tpp) cc_final: 0.7251 (mmm) REVERT: A 603 MET cc_start: 0.8476 (tpp) cc_final: 0.8144 (tpp) REVERT: B 128 GLN cc_start: 0.8045 (tt0) cc_final: 0.7690 (tp40) REVERT: B 146 ARG cc_start: 0.7700 (ttp-110) cc_final: 0.6394 (mtt90) REVERT: B 294 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7610 (tt0) REVERT: B 364 ASP cc_start: 0.8177 (t70) cc_final: 0.7914 (t0) REVERT: B 435 LEU cc_start: 0.8930 (tp) cc_final: 0.8624 (tp) REVERT: B 453 PRO cc_start: 0.9015 (Cg_exo) cc_final: 0.8752 (Cg_endo) REVERT: B 501 ILE cc_start: 0.8862 (tt) cc_final: 0.8616 (tp) REVERT: C 315 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 317 VAL cc_start: 0.8907 (m) cc_final: 0.8580 (p) REVERT: C 318 SER cc_start: 0.8608 (m) cc_final: 0.8189 (t) REVERT: C 432 TYR cc_start: 0.8480 (t80) cc_final: 0.8266 (t80) REVERT: C 435 LEU cc_start: 0.8889 (tp) cc_final: 0.8472 (tt) REVERT: C 474 MET cc_start: 0.7425 (ttm) cc_final: 0.7060 (ttp) REVERT: C 481 MET cc_start: 0.8394 (tpp) cc_final: 0.7993 (tmm) REVERT: C 497 MET cc_start: 0.8678 (ttp) cc_final: 0.8429 (ttp) REVERT: C 592 LEU cc_start: 0.8749 (tp) cc_final: 0.8472 (tt) REVERT: D 42 GLU cc_start: 0.8733 (tp30) cc_final: 0.8354 (tp30) REVERT: D 54 LYS cc_start: 0.8057 (tttm) cc_final: 0.7707 (tmtt) REVERT: D 128 GLN cc_start: 0.7805 (tt0) cc_final: 0.7554 (tp40) REVERT: D 146 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.6472 (mmt90) REVERT: D 246 LEU cc_start: 0.9229 (tp) cc_final: 0.8981 (tt) REVERT: D 315 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7225 (mm-30) REVERT: D 481 MET cc_start: 0.8304 (tpp) cc_final: 0.7865 (tpp) REVERT: D 489 ASP cc_start: 0.6944 (m-30) cc_final: 0.6720 (m-30) REVERT: D 596 GLN cc_start: 0.8506 (pt0) cc_final: 0.8132 (pt0) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2516 time to fit residues: 178.9524 Evaluate side-chains 358 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.203 ------------------------------------------------------------------------------- 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: 4.9990 chunk 172 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 192 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126889 restraints weight = 38094.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129851 restraints weight = 21748.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131811 restraints weight = 14462.800| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18928 Z= 0.214 Angle : 0.651 11.519 25772 Z= 0.317 Chirality : 0.042 0.241 2964 Planarity : 0.004 0.038 3252 Dihedral : 6.624 97.123 2612 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -0.58 (0.18), residues: 2368 helix: 0.89 (0.14), residues: 1388 sheet: -1.44 (0.66), residues: 56 loop : -2.38 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 286 HIS 0.003 0.001 HIS D 258 PHE 0.023 0.002 PHE C 456 TYR 0.018 0.001 TYR B 161 ARG 0.007 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3922.35 seconds wall clock time: 71 minutes 10.51 seconds (4270.51 seconds total)