Starting phenix.real_space_refine on Wed Feb 14 05:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2024/7z0z_14435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2024/7z0z_14435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2024/7z0z_14435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2024/7z0z_14435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2024/7z0z_14435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2024/7z0z_14435.pdb" } resolution = 2.68 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= 0.004 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 29130 atoms to isotropic. 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 114 5.16 5 C 19122 2.51 5 N 4722 2.21 5 O 5508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C ARG 521": "NH1" <-> "NH2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D GLU 328": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "E ARG 521": "NH1" <-> "NH2" Residue "E PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F GLU 583": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29466 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 11.02, per 1000 atoms: 0.37 Number of scatterers: 29466 At special positions: 0 Unit cell: (163.18, 147.6, 115.62, 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 114 16.00 O 5508 8.00 N 4722 7.00 C 19122 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: 9.81 Conformation dependent library (CDL) restraints added in 3.6 seconds 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 64.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 0 through 13 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR A 282 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 310 through 331 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 402 Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 435 through 449 Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'B' and resid 1 through 13 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 273 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 402 Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 517 through 530 Processing helix chain 'B' and resid 534 through 545 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'C' and resid 1 through 13 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 273 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 310 through 331 Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 354 through 364 Processing helix chain 'C' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 402 Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 435 through 449 Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 517 through 530 Processing helix chain 'C' and resid 534 through 545 Processing helix chain 'C' and resid 559 through 564 Processing helix chain 'C' and resid 570 through 582 Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 273 Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR D 282 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 310 through 331 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 354 through 364 Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 402 Processing helix chain 'D' and resid 404 through 419 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 517 through 530 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 559 through 564 Processing helix chain 'D' and resid 570 through 582 Processing helix chain 'E' and resid 1 through 13 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 122 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.198A pdb=" N TRP E 178 " --> pdb=" O HIS E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG E 221 " --> pdb=" O ASN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 273 Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR E 282 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 310 through 331 Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'E' and resid 354 through 364 Processing helix chain 'E' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 402 Processing helix chain 'E' and resid 404 through 419 Processing helix chain 'E' and resid 419 through 434 Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 504 removed outlier: 3.538A pdb=" N LYS E 494 " --> pdb=" O LYS E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 517 through 530 Processing helix chain 'E' and resid 534 through 545 Processing helix chain 'E' and resid 559 through 564 Processing helix chain 'E' and resid 570 through 582 Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.826A pdb=" N SER F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG F 221 " --> pdb=" O ASN F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 273 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR F 282 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 310 through 331 Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 354 through 364 Processing helix chain 'F' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 402 Processing helix chain 'F' and resid 404 through 419 Processing helix chain 'F' and resid 419 through 434 Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 462 through 464 No H-bonds generated for 'chain 'F' and resid 462 through 464' Processing helix chain 'F' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS F 494 " --> pdb=" O LYS F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 517 through 530 Processing helix chain 'F' and resid 534 through 545 Processing helix chain 'F' and resid 559 through 564 Processing helix chain 'F' and resid 570 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 245 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 89 Processing sheet with id=AA6, first strand: chain 'C' and resid 243 through 245 Processing sheet with id=AA7, first strand: chain 'D' and resid 84 through 89 Processing sheet with id=AA8, first strand: chain 'D' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'E' and resid 84 through 89 Processing sheet with id=AB1, first strand: chain 'E' and resid 243 through 245 Processing sheet with id=AB2, first strand: chain 'F' and resid 84 through 89 Processing sheet with id=AB3, first strand: chain 'F' and resid 243 through 245 1567 hydrogen bonds defined for protein. 4485 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: 7.59 Time building geometry restraints manager: 10.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4865 1.31 - 1.43: 8737 1.43 - 1.56: 16404 1.56 - 1.68: 0 1.68 - 1.81: 174 Bond restraints: 30180 Sorted by residual: bond pdb=" C TYR D 245 " pdb=" O TYR D 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" C TYR F 245 " pdb=" O TYR F 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.81e+01 bond pdb=" C TYR A 245 " pdb=" O TYR A 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.80e+01 bond pdb=" C TYR C 245 " pdb=" O TYR C 245 " ideal model delta sigma weight residual 1.236 1.186 0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" C TYR E 245 " pdb=" O TYR E 245 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.17e-02 7.31e+03 1.76e+01 ... (remaining 30175 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.33: 442 106.33 - 113.27: 15669 113.27 - 120.21: 11821 120.21 - 127.15: 12538 127.15 - 134.08: 198 Bond angle restraints: 40668 Sorted by residual: angle pdb=" N GLU B 489 " pdb=" CA GLU B 489 " pdb=" C GLU B 489 " ideal model delta sigma weight residual 114.56 102.69 11.87 1.27e+00 6.20e-01 8.73e+01 angle pdb=" N GLU A 489 " pdb=" CA GLU A 489 " pdb=" C GLU A 489 " ideal model delta sigma weight residual 114.56 102.70 11.86 1.27e+00 6.20e-01 8.72e+01 angle pdb=" N GLU E 489 " pdb=" CA GLU E 489 " pdb=" C GLU E 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.71e+01 angle pdb=" N GLU C 489 " pdb=" CA GLU C 489 " pdb=" C GLU C 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.70e+01 angle pdb=" N GLU D 489 " pdb=" CA GLU D 489 " pdb=" C GLU D 489 " ideal model delta sigma weight residual 114.56 102.72 11.84 1.27e+00 6.20e-01 8.69e+01 ... (remaining 40663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 16137 18.02 - 36.04: 1404 36.04 - 54.06: 246 54.06 - 72.08: 63 72.08 - 90.10: 54 Dihedral angle restraints: 17904 sinusoidal: 7398 harmonic: 10506 Sorted by residual: dihedral pdb=" C VAL A 246 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " pdb=" CB VAL A 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL F 246 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " pdb=" CB VAL F 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL E 246 " pdb=" N VAL E 246 " pdb=" CA VAL E 246 " pdb=" CB VAL E 246 " ideal model delta harmonic sigma weight residual -122.00 -135.84 13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 17901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3829 0.078 - 0.155: 429 0.155 - 0.233: 32 0.233 - 0.311: 6 0.311 - 0.389: 6 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CA VAL E 246 " pdb=" N VAL E 246 " pdb=" C VAL E 246 " pdb=" CB VAL E 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL B 246 " pdb=" N VAL B 246 " pdb=" C VAL B 246 " pdb=" CB VAL B 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA VAL F 246 " pdb=" N VAL F 246 " pdb=" C VAL F 246 " pdb=" CB VAL F 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 4299 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA D 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA D 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER D 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA E 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA E 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER E 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 185 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ALA A 185 " 0.071 2.00e-02 2.50e+03 pdb=" O ALA A 185 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 186 " -0.024 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 372 2.65 - 3.22: 28315 3.22 - 3.78: 47268 3.78 - 4.34: 70523 4.34 - 4.90: 112653 Nonbonded interactions: 259131 Sorted by model distance: nonbonded pdb=" OH TYR E 522 " pdb=" O VAL E 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR F 522 " pdb=" O VAL F 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR C 522 " pdb=" O VAL C 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR A 522 " pdb=" O VAL A 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR D 522 " pdb=" O VAL D 584 " model vdw 2.092 2.440 ... (remaining 259126 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 11.420 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 57.730 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.130 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:9.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.006 0.072 30180 Z= 0.378 Angle : 0.718 11.868 40668 Z= 0.446 Chirality : 0.053 0.389 4302 Planarity : 0.004 0.041 5190 Dihedral : 14.672 90.096 11112 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.87 % Favored : 97.96 % Rotamer: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.91 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 9.09 % 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: 0.45 (0.14), residues: 3474 helix: 0.82 (0.11), residues: 2124 sheet: 0.80 (0.41), residues: 156 loop : -0.59 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 585 HIS 0.005 0.001 HIS D 67 PHE 0.026 0.002 PHE E 44 TYR 0.029 0.002 TYR E 106 ARG 0.003 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 558 time to evaluate : 2.636 Fit side-chains REVERT: A 208 ASP cc_start: 0.8174 (m-30) cc_final: 0.7971 (m-30) REVERT: B 3 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8247 (tttm) REVERT: B 488 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7764 (mt) REVERT: B 548 ASN cc_start: 0.7717 (t0) cc_final: 0.7493 (t0) REVERT: C 228 MET cc_start: 0.8932 (mmp) cc_final: 0.8717 (mmp) REVERT: C 280 ASN cc_start: 0.7940 (m110) cc_final: 0.7586 (m-40) REVERT: C 488 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7783 (mt) REVERT: D 248 ASP cc_start: 0.6629 (t0) cc_final: 0.6427 (t0) REVERT: D 280 ASN cc_start: 0.7774 (m110) cc_final: 0.7506 (m110) REVERT: E 21 TYR cc_start: 0.8994 (m-80) cc_final: 0.8701 (m-80) REVERT: E 488 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7646 (mt) REVERT: F 3 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8353 (tttm) REVERT: F 488 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7755 (mt) REVERT: F 548 ASN cc_start: 0.7705 (t0) cc_final: 0.7496 (t0) outliers start: 18 outliers final: 2 residues processed: 561 average time/residue: 1.2509 time to fit residues: 807.9967 Evaluate side-chains 400 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 394 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 537 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 273 ASN A 389 ASN A 399 ASN A 433 ASN A 505 ASN A 543 GLN B 30 ASN B 273 ASN B 399 ASN B 433 ASN B 436 ASN B 543 GLN C 30 ASN C 87 ASN C 273 ASN C 389 ASN C 399 ASN C 433 ASN C 436 ASN C 548 ASN D 30 ASN D 87 ASN D 273 ASN D 280 ASN D 286 ASN D 389 ASN D 399 ASN D 433 ASN D 436 ASN D 548 ASN E 30 ASN E 87 ASN E 110 ASN E 273 ASN E 399 ASN E 433 ASN E 436 ASN E 543 GLN F 30 ASN F 67 HIS F 110 ASN F 273 ASN F 399 ASN F 433 ASN F 436 ASN F 543 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30180 Z= 0.222 Angle : 0.481 5.678 40668 Z= 0.267 Chirality : 0.041 0.144 4302 Planarity : 0.003 0.037 5190 Dihedral : 4.501 37.293 3812 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.41 % Favored : 98.42 % Rotamer: Outliers : 1.42 % Allowed : 8.86 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.87 (0.15), residues: 3474 helix: 1.14 (0.11), residues: 2190 sheet: 0.69 (0.44), residues: 156 loop : -0.41 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 585 HIS 0.004 0.001 HIS F 67 PHE 0.016 0.002 PHE D 231 TYR 0.016 0.002 TYR C 525 ARG 0.007 0.001 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 448 time to evaluate : 2.572 Fit side-chains REVERT: A 29 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7507 (mmpt) REVERT: A 208 ASP cc_start: 0.8156 (m-30) cc_final: 0.7941 (m-30) REVERT: A 568 LYS cc_start: 0.8756 (ptmm) cc_final: 0.8229 (pmtt) REVERT: B 3 LYS cc_start: 0.8523 (ttpp) cc_final: 0.8275 (tttm) REVERT: B 233 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7974 (ttpp) REVERT: B 548 ASN cc_start: 0.7761 (t0) cc_final: 0.7547 (t0) REVERT: B 568 LYS cc_start: 0.8801 (ptmm) cc_final: 0.8301 (pmtt) REVERT: C 2 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7338 (mptm) REVERT: C 29 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7538 (tptt) REVERT: C 283 LYS cc_start: 0.8413 (pttm) cc_final: 0.8022 (ptpt) REVERT: D 146 GLN cc_start: 0.7991 (mm110) cc_final: 0.7691 (mm-40) REVERT: D 568 LYS cc_start: 0.8672 (ptmm) cc_final: 0.8206 (pmtt) REVERT: E 21 TYR cc_start: 0.9002 (m-80) cc_final: 0.8642 (m-80) REVERT: E 317 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7593 (mm-30) REVERT: F 3 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8326 (tttm) REVERT: F 356 LYS cc_start: 0.8189 (mppt) cc_final: 0.7896 (mppt) REVERT: F 537 GLU cc_start: 0.6579 (tp30) cc_final: 0.6355 (OUTLIER) REVERT: F 568 LYS cc_start: 0.8808 (ptmm) cc_final: 0.8230 (pmtt) outliers start: 47 outliers final: 15 residues processed: 466 average time/residue: 1.1728 time to fit residues: 636.7397 Evaluate side-chains 410 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 394 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain F residue 236 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 263 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 316 optimal weight: 0.8980 chunk 342 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 313 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 110 ASN A 436 ASN A 543 GLN B 30 ASN B 87 ASN C 30 ASN C 110 ASN C 280 ASN C 548 ASN D 30 ASN D 110 ASN D 548 ASN E 30 ASN E 110 ASN E 543 GLN F 30 ASN F 67 HIS F 87 ASN F 110 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30180 Z= 0.160 Angle : 0.429 5.649 40668 Z= 0.239 Chirality : 0.039 0.140 4302 Planarity : 0.003 0.036 5190 Dihedral : 4.158 44.551 3801 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.61 % Favored : 98.22 % Rotamer: Outliers : 1.54 % Allowed : 10.25 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.14 (0.15), residues: 3474 helix: 1.40 (0.11), residues: 2190 sheet: 0.46 (0.44), residues: 156 loop : -0.36 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 585 HIS 0.003 0.001 HIS C 230 PHE 0.014 0.001 PHE D 231 TYR 0.014 0.001 TYR B 227 ARG 0.008 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 426 time to evaluate : 2.580 Fit side-chains REVERT: A 276 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8523 (mm) REVERT: A 568 LYS cc_start: 0.8759 (ptmm) cc_final: 0.8239 (pmtt) REVERT: B 3 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8273 (tttm) REVERT: B 209 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: B 233 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7912 (ttpp) REVERT: B 356 LYS cc_start: 0.8232 (mppt) cc_final: 0.8027 (mppt) REVERT: B 548 ASN cc_start: 0.7761 (t0) cc_final: 0.7540 (t0) REVERT: B 568 LYS cc_start: 0.8763 (ptmm) cc_final: 0.8335 (pmtt) REVERT: C 2 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7384 (mptm) REVERT: C 283 LYS cc_start: 0.8391 (pttm) cc_final: 0.7991 (ptpt) REVERT: C 356 LYS cc_start: 0.8064 (mppt) cc_final: 0.7678 (mmtm) REVERT: D 146 GLN cc_start: 0.8009 (mm110) cc_final: 0.7708 (mm-40) REVERT: D 568 LYS cc_start: 0.8655 (ptmm) cc_final: 0.8185 (pmtt) REVERT: D 591 GLU cc_start: 0.7242 (pt0) cc_final: 0.6903 (mp0) REVERT: E 317 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7590 (mm-30) REVERT: F 1 MET cc_start: 0.7733 (ttm) cc_final: 0.7202 (ttm) REVERT: F 4 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7380 (mp0) REVERT: F 209 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: F 356 LYS cc_start: 0.8205 (mppt) cc_final: 0.7973 (mptt) REVERT: F 490 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8575 (mtmt) REVERT: F 548 ASN cc_start: 0.7648 (t0) cc_final: 0.7439 (t0) REVERT: F 568 LYS cc_start: 0.8769 (ptmm) cc_final: 0.8222 (pmtt) outliers start: 51 outliers final: 11 residues processed: 451 average time/residue: 1.1323 time to fit residues: 597.2733 Evaluate side-chains 413 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 398 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 490 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 35 optimal weight: 0.0050 chunk 151 optimal weight: 4.9990 chunk 212 optimal weight: 0.6980 chunk 317 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN B 30 ASN C 30 ASN C 110 ASN C 311 ASN C 548 ASN D 30 ASN D 280 ASN D 548 ASN E 30 ASN E 110 ASN E 260 GLN E 543 GLN F 30 ASN F 67 HIS F 110 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30180 Z= 0.154 Angle : 0.418 5.554 40668 Z= 0.232 Chirality : 0.039 0.139 4302 Planarity : 0.003 0.036 5190 Dihedral : 3.931 20.893 3798 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.53 % Favored : 98.30 % Rotamer: Outliers : 1.88 % Allowed : 10.62 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.32 (0.15), residues: 3474 helix: 1.56 (0.11), residues: 2190 sheet: 0.32 (0.44), residues: 156 loop : -0.32 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 585 HIS 0.003 0.001 HIS A 230 PHE 0.013 0.001 PHE D 231 TYR 0.013 0.001 TYR B 227 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 417 time to evaluate : 2.606 Fit side-chains REVERT: A 276 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 548 ASN cc_start: 0.7892 (t0) cc_final: 0.7664 (t0) REVERT: A 568 LYS cc_start: 0.8737 (ptmm) cc_final: 0.8248 (pmtt) REVERT: B 3 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8279 (tttm) REVERT: B 169 HIS cc_start: 0.7805 (m-70) cc_final: 0.7604 (m-70) REVERT: B 209 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: B 356 LYS cc_start: 0.8206 (mppt) cc_final: 0.7864 (mptt) REVERT: B 548 ASN cc_start: 0.7758 (t0) cc_final: 0.7534 (t0) REVERT: B 568 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8375 (pmtt) REVERT: C 2 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7460 (mptm) REVERT: C 283 LYS cc_start: 0.8395 (pttm) cc_final: 0.7987 (ptpt) REVERT: C 356 LYS cc_start: 0.8092 (mppt) cc_final: 0.7686 (mmtm) REVERT: D 146 GLN cc_start: 0.8001 (mm110) cc_final: 0.7686 (mm-40) REVERT: D 568 LYS cc_start: 0.8677 (ptmm) cc_final: 0.8214 (pmtt) REVERT: D 591 GLU cc_start: 0.7234 (pt0) cc_final: 0.6905 (mp0) REVERT: E 4 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: E 317 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7614 (mm-30) REVERT: E 487 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7822 (mmmt) REVERT: E 497 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7651 (mm-40) REVERT: F 1 MET cc_start: 0.7660 (ttm) cc_final: 0.7125 (ttm) REVERT: F 4 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7339 (mp0) REVERT: F 209 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: F 356 LYS cc_start: 0.8209 (mppt) cc_final: 0.7839 (mptt) REVERT: F 548 ASN cc_start: 0.7693 (t0) cc_final: 0.7451 (t0) REVERT: F 568 LYS cc_start: 0.8762 (ptmm) cc_final: 0.8233 (pmtt) outliers start: 62 outliers final: 13 residues processed: 450 average time/residue: 1.1793 time to fit residues: 618.6132 Evaluate side-chains 417 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 399 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 487 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 367 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 287 optimal weight: 0.0040 chunk 232 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 301 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 543 GLN B 30 ASN B 87 ASN C 30 ASN C 280 ASN C 548 ASN D 30 ASN D 548 ASN E 280 ASN E 543 GLN E 548 ASN F 30 ASN F 67 HIS F 87 ASN F 311 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30180 Z= 0.197 Angle : 0.437 8.926 40668 Z= 0.242 Chirality : 0.040 0.141 4302 Planarity : 0.003 0.035 5190 Dihedral : 3.953 22.600 3798 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.84 % Favored : 97.99 % Rotamer: Outliers : 1.94 % Allowed : 11.31 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.32 (0.15), residues: 3474 helix: 1.57 (0.11), residues: 2190 sheet: 0.19 (0.43), residues: 156 loop : -0.31 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 585 HIS 0.004 0.001 HIS D 230 PHE 0.015 0.001 PHE D 231 TYR 0.012 0.001 TYR F 227 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 411 time to evaluate : 2.697 Fit side-chains REVERT: A 276 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 568 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8239 (pmtt) REVERT: B 3 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8312 (tttm) REVERT: B 209 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: B 356 LYS cc_start: 0.8237 (mppt) cc_final: 0.8024 (mppt) REVERT: B 548 ASN cc_start: 0.7778 (t0) cc_final: 0.7555 (t0) REVERT: B 568 LYS cc_start: 0.8732 (ptmm) cc_final: 0.8361 (pmtt) REVERT: B 591 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: C 2 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7452 (mptm) REVERT: C 283 LYS cc_start: 0.8414 (pttm) cc_final: 0.8007 (ptpt) REVERT: C 579 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8136 (mp) REVERT: D 118 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8252 (mptt) REVERT: D 146 GLN cc_start: 0.8024 (mm110) cc_final: 0.7696 (mm-40) REVERT: D 257 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7263 (p0) REVERT: D 568 LYS cc_start: 0.8673 (ptmm) cc_final: 0.8225 (pmtt) REVERT: D 591 GLU cc_start: 0.7250 (pt0) cc_final: 0.6908 (mp0) REVERT: E 4 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: E 317 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7623 (mm-30) REVERT: E 490 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8551 (mtpt) REVERT: E 497 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7653 (mm-40) REVERT: F 1 MET cc_start: 0.7652 (ttm) cc_final: 0.7188 (ttm) REVERT: F 4 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7358 (mp0) REVERT: F 209 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: F 356 LYS cc_start: 0.8199 (mppt) cc_final: 0.7863 (mptt) REVERT: F 548 ASN cc_start: 0.7695 (t0) cc_final: 0.7425 (t0) REVERT: F 568 LYS cc_start: 0.8770 (ptmm) cc_final: 0.8254 (pmtt) REVERT: F 591 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6400 (mp0) outliers start: 64 outliers final: 26 residues processed: 444 average time/residue: 1.1850 time to fit residues: 611.4723 Evaluate side-chains 426 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 391 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 490 LYS Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 591 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.2980 chunk 302 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 111 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 110 ASN A 257 ASN B 30 ASN B 110 ASN B 169 HIS B 217 ASN B 311 ASN B 543 GLN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 30 ASN E 67 HIS E 110 ASN E 543 GLN E 548 ASN F 30 ASN F 67 HIS ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30180 Z= 0.160 Angle : 0.421 6.708 40668 Z= 0.233 Chirality : 0.039 0.139 4302 Planarity : 0.003 0.034 5190 Dihedral : 3.867 20.843 3798 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.84 % Favored : 97.99 % Rotamer: Outliers : 2.03 % Allowed : 11.55 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.15), residues: 3474 helix: 1.63 (0.11), residues: 2190 sheet: 0.13 (0.43), residues: 156 loop : -0.29 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 585 HIS 0.007 0.001 HIS E 67 PHE 0.014 0.001 PHE E 231 TYR 0.014 0.001 TYR B 227 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 402 time to evaluate : 2.618 Fit side-chains REVERT: A 276 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 548 ASN cc_start: 0.7873 (t0) cc_final: 0.7640 (t0) REVERT: A 568 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8235 (pmtt) REVERT: B 3 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8302 (tttm) REVERT: B 146 GLN cc_start: 0.7847 (mm110) cc_final: 0.7502 (mm-40) REVERT: B 209 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: B 356 LYS cc_start: 0.8251 (mppt) cc_final: 0.7867 (mptt) REVERT: B 490 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8169 (mtmt) REVERT: B 548 ASN cc_start: 0.7782 (t0) cc_final: 0.7561 (t0) REVERT: B 568 LYS cc_start: 0.8730 (ptmm) cc_final: 0.8370 (pmtt) REVERT: B 591 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: C 2 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7468 (mptm) REVERT: C 350 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: C 356 LYS cc_start: 0.8109 (mppt) cc_final: 0.7755 (mmtm) REVERT: C 561 ASN cc_start: 0.8700 (m-40) cc_final: 0.8429 (m-40) REVERT: C 579 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8166 (mp) REVERT: D 118 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8265 (mptt) REVERT: D 146 GLN cc_start: 0.7989 (mm110) cc_final: 0.7689 (mm-40) REVERT: D 568 LYS cc_start: 0.8670 (ptmm) cc_final: 0.8235 (pmtt) REVERT: D 591 GLU cc_start: 0.7252 (pt0) cc_final: 0.6937 (mp0) REVERT: E 4 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: E 317 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7614 (mm-30) REVERT: E 497 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7618 (mm-40) REVERT: E 591 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: F 1 MET cc_start: 0.7646 (ttm) cc_final: 0.7190 (ttm) REVERT: F 4 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7366 (mp0) REVERT: F 209 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: F 356 LYS cc_start: 0.8228 (mppt) cc_final: 0.8019 (mptt) REVERT: F 490 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8135 (mtmt) REVERT: F 548 ASN cc_start: 0.7735 (t0) cc_final: 0.7445 (t0) REVERT: F 568 LYS cc_start: 0.8755 (ptmm) cc_final: 0.8241 (pmtt) REVERT: F 591 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6411 (mp0) outliers start: 67 outliers final: 25 residues processed: 440 average time/residue: 1.1708 time to fit residues: 601.3639 Evaluate side-chains 426 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 390 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 490 LYS Chi-restraints excluded: chain F residue 543 GLN Chi-restraints excluded: chain F residue 591 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 280 ASN A 311 ASN A 360 ASN A 543 GLN B 30 ASN B 110 ASN B 543 GLN C 30 ASN C 548 ASN D 30 ASN D 217 ASN D 311 ASN D 360 ASN D 543 GLN D 548 ASN E 30 ASN E 543 GLN E 548 ASN F 30 ASN F 67 HIS F 110 ASN F 543 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 30180 Z= 0.356 Angle : 0.501 6.164 40668 Z= 0.275 Chirality : 0.043 0.147 4302 Planarity : 0.003 0.036 5190 Dihedral : 4.142 24.363 3798 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.19 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 11.52 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.14 (0.15), residues: 3474 helix: 1.40 (0.11), residues: 2184 sheet: 0.09 (0.42), residues: 156 loop : -0.30 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 585 HIS 0.006 0.001 HIS C 230 PHE 0.018 0.002 PHE E 231 TYR 0.015 0.002 TYR C 227 ARG 0.004 0.001 ARG F 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 403 time to evaluate : 2.784 Fit side-chains REVERT: A 257 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7528 (p0) REVERT: A 276 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 568 LYS cc_start: 0.8708 (ptmm) cc_final: 0.8229 (pmtt) REVERT: B 209 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: B 431 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (mtp-110) REVERT: B 490 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8286 (mtmt) REVERT: B 548 ASN cc_start: 0.7799 (t0) cc_final: 0.7552 (t0) REVERT: B 568 LYS cc_start: 0.8748 (ptmm) cc_final: 0.8384 (pmtt) REVERT: B 591 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: C 2 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7460 (mptm) REVERT: D 146 GLN cc_start: 0.8033 (mm110) cc_final: 0.7712 (mm-40) REVERT: D 257 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7366 (p0) REVERT: D 568 LYS cc_start: 0.8692 (ptmm) cc_final: 0.8252 (pmtt) REVERT: D 591 GLU cc_start: 0.7295 (pt0) cc_final: 0.6958 (mp0) REVERT: E 4 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: E 317 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7617 (mm-30) REVERT: E 497 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7622 (mm-40) REVERT: E 591 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: F 4 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7403 (mp0) REVERT: F 209 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: F 356 LYS cc_start: 0.8234 (mppt) cc_final: 0.7933 (mptt) REVERT: F 431 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8038 (mtp-110) REVERT: F 490 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8297 (mtmt) REVERT: F 548 ASN cc_start: 0.7745 (t0) cc_final: 0.7439 (t0) REVERT: F 568 LYS cc_start: 0.8771 (ptmm) cc_final: 0.8266 (pmtt) outliers start: 69 outliers final: 26 residues processed: 440 average time/residue: 1.2291 time to fit residues: 631.6904 Evaluate side-chains 424 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 386 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 543 GLN Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 490 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 110 ASN A 217 ASN A 280 ASN A 311 ASN A 360 ASN B 110 ASN B 543 GLN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 543 GLN E 548 ASN F 30 ASN F 67 HIS F 110 ASN F 543 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30180 Z= 0.193 Angle : 0.440 6.728 40668 Z= 0.243 Chirality : 0.039 0.142 4302 Planarity : 0.003 0.035 5190 Dihedral : 3.999 23.618 3798 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.70 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 11.86 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.24 (0.15), residues: 3474 helix: 1.50 (0.11), residues: 2184 sheet: 0.02 (0.42), residues: 156 loop : -0.30 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 585 HIS 0.003 0.001 HIS A 230 PHE 0.014 0.001 PHE D 231 TYR 0.016 0.001 TYR E 227 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 398 time to evaluate : 2.616 Fit side-chains REVERT: A 276 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8495 (mm) REVERT: A 568 LYS cc_start: 0.8707 (ptmm) cc_final: 0.8278 (pmtt) REVERT: B 1 MET cc_start: 0.7931 (ttm) cc_final: 0.7650 (ttm) REVERT: B 209 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: B 356 LYS cc_start: 0.8203 (mppt) cc_final: 0.7987 (mptt) REVERT: B 431 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7914 (mtp180) REVERT: B 548 ASN cc_start: 0.7802 (t0) cc_final: 0.7557 (t0) REVERT: B 568 LYS cc_start: 0.8722 (ptmm) cc_final: 0.8370 (pmtt) REVERT: B 591 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: C 2 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7436 (mptm) REVERT: C 356 LYS cc_start: 0.8130 (mppt) cc_final: 0.7889 (mptp) REVERT: C 497 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: C 579 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8213 (mp) REVERT: D 118 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8258 (mptt) REVERT: D 146 GLN cc_start: 0.8009 (mm110) cc_final: 0.7703 (mm-40) REVERT: D 257 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7360 (p0) REVERT: D 568 LYS cc_start: 0.8692 (ptmm) cc_final: 0.8242 (pmtt) REVERT: D 591 GLU cc_start: 0.7284 (pt0) cc_final: 0.6950 (mp0) REVERT: E 4 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: E 317 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7615 (mm-30) REVERT: E 497 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7621 (mm-40) REVERT: E 591 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: F 209 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: F 356 LYS cc_start: 0.8198 (mppt) cc_final: 0.7949 (mptt) REVERT: F 431 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8005 (mtp-110) REVERT: F 548 ASN cc_start: 0.7760 (t0) cc_final: 0.7458 (t0) REVERT: F 568 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8254 (pmtt) outliers start: 68 outliers final: 29 residues processed: 436 average time/residue: 1.1610 time to fit residues: 590.5280 Evaluate side-chains 425 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 385 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 543 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.6980 chunk 321 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 312 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 311 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 543 GLN B 87 ASN B 110 ASN B 543 GLN C 30 ASN C 110 ASN D 30 ASN D 217 ASN D 543 GLN D 548 ASN E 30 ASN E 110 ASN F 30 ASN F 67 HIS F 110 ASN F 217 ASN F 543 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30180 Z= 0.186 Angle : 0.442 6.824 40668 Z= 0.243 Chirality : 0.039 0.142 4302 Planarity : 0.003 0.035 5190 Dihedral : 3.944 21.850 3798 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.96 % Favored : 97.87 % Rotamer: Outliers : 1.51 % Allowed : 12.70 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.29 (0.15), residues: 3474 helix: 1.54 (0.11), residues: 2184 sheet: 0.01 (0.42), residues: 156 loop : -0.28 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 585 HIS 0.003 0.001 HIS A 230 PHE 0.014 0.001 PHE C 231 TYR 0.013 0.001 TYR F 227 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 394 time to evaluate : 2.604 Fit side-chains REVERT: A 146 GLN cc_start: 0.8011 (mm110) cc_final: 0.7674 (mm-40) REVERT: A 276 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8478 (mm) REVERT: A 568 LYS cc_start: 0.8705 (ptmm) cc_final: 0.8280 (pmtt) REVERT: B 1 MET cc_start: 0.7893 (ttm) cc_final: 0.7671 (ttm) REVERT: B 146 GLN cc_start: 0.7815 (mm110) cc_final: 0.7484 (mm-40) REVERT: B 209 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 356 LYS cc_start: 0.8185 (mppt) cc_final: 0.7961 (mptt) REVERT: B 431 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8017 (mtp-110) REVERT: B 492 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 548 ASN cc_start: 0.7799 (t0) cc_final: 0.7554 (t0) REVERT: B 568 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8372 (pmtt) REVERT: B 591 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: C 2 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7435 (mptm) REVERT: C 356 LYS cc_start: 0.8136 (mppt) cc_final: 0.7897 (mptp) REVERT: C 497 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: C 579 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8207 (mp) REVERT: D 118 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8278 (mptt) REVERT: D 146 GLN cc_start: 0.7958 (mm110) cc_final: 0.7667 (mm-40) REVERT: D 257 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7361 (p0) REVERT: D 568 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8265 (pmtt) REVERT: D 591 GLU cc_start: 0.7278 (pt0) cc_final: 0.6945 (mp0) REVERT: E 4 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: E 317 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7622 (mm-30) REVERT: E 356 LYS cc_start: 0.8164 (mppt) cc_final: 0.7915 (mptp) REVERT: E 497 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7623 (mm-40) REVERT: E 591 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: F 209 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: F 356 LYS cc_start: 0.8201 (mppt) cc_final: 0.7848 (mptt) REVERT: F 548 ASN cc_start: 0.7755 (t0) cc_final: 0.7448 (t0) REVERT: F 568 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8251 (pmtt) outliers start: 50 outliers final: 28 residues processed: 425 average time/residue: 1.1868 time to fit residues: 588.2122 Evaluate side-chains 426 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 387 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 367 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 543 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 346 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN B 110 ASN B 543 GLN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 30 ASN E 110 ASN E 543 GLN E 548 ASN F 30 ASN F 67 HIS F 87 ASN F 97 GLN F 110 ASN F 543 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30180 Z= 0.190 Angle : 0.443 6.980 40668 Z= 0.244 Chirality : 0.039 0.142 4302 Planarity : 0.003 0.034 5190 Dihedral : 3.932 22.021 3798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.96 % Favored : 97.87 % Rotamer: Outliers : 1.48 % Allowed : 12.86 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.29 (0.15), residues: 3474 helix: 1.53 (0.11), residues: 2190 sheet: 0.01 (0.42), residues: 156 loop : -0.25 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 585 HIS 0.004 0.001 HIS F 67 PHE 0.014 0.001 PHE E 231 TYR 0.013 0.001 TYR F 227 ARG 0.002 0.000 ARG F 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 394 time to evaluate : 2.620 Fit side-chains REVERT: A 146 GLN cc_start: 0.8027 (mm110) cc_final: 0.7694 (mm-40) REVERT: A 257 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7499 (p0) REVERT: A 276 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8478 (mm) REVERT: A 568 LYS cc_start: 0.8704 (ptmm) cc_final: 0.8276 (pmtt) REVERT: B 146 GLN cc_start: 0.7813 (mm110) cc_final: 0.7497 (mm-40) REVERT: B 209 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: B 356 LYS cc_start: 0.8175 (mppt) cc_final: 0.7950 (mptt) REVERT: B 431 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8016 (mtp-110) REVERT: B 492 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 548 ASN cc_start: 0.7801 (t0) cc_final: 0.7553 (t0) REVERT: B 568 LYS cc_start: 0.8734 (ptmm) cc_final: 0.8378 (pmtt) REVERT: B 591 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: C 2 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7443 (mptm) REVERT: C 356 LYS cc_start: 0.8133 (mppt) cc_final: 0.7890 (mptp) REVERT: C 497 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: C 579 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8204 (mp) REVERT: D 118 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8277 (mptt) REVERT: D 146 GLN cc_start: 0.7963 (mm110) cc_final: 0.7677 (mm-40) REVERT: D 257 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7364 (p0) REVERT: D 568 LYS cc_start: 0.8706 (ptmm) cc_final: 0.8265 (pmtt) REVERT: D 591 GLU cc_start: 0.7262 (pt0) cc_final: 0.6934 (mp0) REVERT: E 4 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: E 317 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7622 (mm-30) REVERT: E 356 LYS cc_start: 0.8156 (mppt) cc_final: 0.7946 (mptp) REVERT: E 497 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7625 (mm-40) REVERT: E 591 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: F 146 GLN cc_start: 0.7873 (mm110) cc_final: 0.7562 (mm-40) REVERT: F 209 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: F 356 LYS cc_start: 0.8203 (mppt) cc_final: 0.7850 (mptt) REVERT: F 548 ASN cc_start: 0.7743 (t0) cc_final: 0.7439 (t0) REVERT: F 568 LYS cc_start: 0.8738 (ptmm) cc_final: 0.8245 (pmtt) outliers start: 49 outliers final: 26 residues processed: 427 average time/residue: 1.1712 time to fit residues: 583.0969 Evaluate side-chains 425 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 387 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 367 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 276 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 283 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 543 GLN B 110 ASN B 543 GLN C 30 ASN D 30 ASN D 217 ASN D 543 GLN D 548 ASN E 30 ASN E 110 ASN E 543 GLN F 67 HIS ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 543 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099709 restraints weight = 36851.373| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.81 r_work: 0.3033 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 30180 Z= 0.206 Angle : 0.586 59.193 40668 Z= 0.340 Chirality : 0.040 0.459 4302 Planarity : 0.003 0.034 5190 Dihedral : 3.944 23.518 3798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 1.48 % Allowed : 12.86 % Favored : 85.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 1.28 (0.15), residues: 3474 helix: 1.52 (0.11), residues: 2190 sheet: 0.01 (0.42), residues: 156 loop : -0.25 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 585 HIS 0.004 0.001 HIS F 67 PHE 0.014 0.001 PHE C 231 TYR 0.013 0.001 TYR F 227 ARG 0.002 0.000 ARG F 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9339.21 seconds wall clock time: 163 minutes 43.79 seconds (9823.79 seconds total)