Starting phenix.real_space_refine (version: dev) on Thu Feb 23 16:30:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/02_2023/7r06_14220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/02_2023/7r06_14220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/02_2023/7r06_14220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/02_2023/7r06_14220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/02_2023/7r06_14220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/02_2023/7r06_14220_updated.pdb" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.303 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 30468 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C ARG 431": "NH1" <-> "NH2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 489": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ARG 521": "NH1" <-> "NH2" Residue "C GLU 537": "OE1" <-> "OE2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 593": "OE1" <-> "OE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D GLU 328": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D GLU 537": "OE1" <-> "OE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "D GLU 593": "OE1" <-> "OE2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 489": "OE1" <-> "OE2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E ARG 521": "NH1" <-> "NH2" Residue "E GLU 537": "OE1" <-> "OE2" Residue "E GLU 557": "OE1" <-> "OE2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "E GLU 593": "OE1" <-> "OE2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F GLU 258": "OE1" <-> "OE2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "F ARG 431": "NH1" <-> "NH2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F GLU 489": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F GLU 537": "OE1" <-> "OE2" Residue "F GLU 557": "OE1" <-> "OE2" Residue "F GLU 583": "OE1" <-> "OE2" Residue "F GLU 593": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31320 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 5015 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'PTR:plan-2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 205 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 5015 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'PTR:plan-2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 205 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 5015 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'PTR:plan-2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 205 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 5015 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'PTR:plan-2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 205 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 5015 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'PTR:plan-2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 205 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 5015 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'PTR:plan-2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 205 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 12.48, per 1000 atoms: 0.40 Number of scatterers: 31320 At special positions: 0 Unit cell: (158.65, 147.25, 114.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 66 15.00 O 6030 8.00 N 5028 7.00 C 20076 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.81 Conformation dependent library (CDL) restraints added in 3.2 seconds 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 12 sheets defined 56.0% alpha, 4.0% beta 0 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 7.67 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.775A pdb=" N SER A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 117 through 126 removed outlier: 4.203A pdb=" N VAL A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 152 Processing helix chain 'A' and resid 167 through 170 No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 173 through 181 Proline residue: A 177 - end of helix removed outlier: 3.554A pdb=" N ILE A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 181 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 218 through 237 Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'A' and resid 336 through 350 removed outlier: 4.532A pdb=" N PHE A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 385 through 401 removed outlier: 4.769A pdb=" N ASN A 389 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.803A pdb=" N ASN A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 518 through 530 Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 560 through 565 removed outlier: 4.584A pdb=" N GLY A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'B' and resid 1 through 12 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.775A pdb=" N SER B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 117 through 126 removed outlier: 4.204A pdb=" N VAL B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 173 through 181 Proline residue: B 177 - end of helix removed outlier: 3.553A pdb=" N ILE B 180 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 181 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 218 through 237 Processing helix chain 'B' and resid 256 through 272 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 336 through 350 removed outlier: 4.533A pdb=" N PHE B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Proline residue: B 342 - end of helix Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 385 through 401 removed outlier: 4.769A pdb=" N ASN B 389 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 436 through 448 Processing helix chain 'B' and resid 457 through 463 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.802A pdb=" N ASN B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 518 through 530 Processing helix chain 'B' and resid 535 through 545 Processing helix chain 'B' and resid 560 through 565 removed outlier: 4.584A pdb=" N GLY B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.774A pdb=" N SER C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 117 through 126 removed outlier: 4.204A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'C' and resid 167 through 170 No H-bonds generated for 'chain 'C' and resid 167 through 170' Processing helix chain 'C' and resid 173 through 181 Proline residue: C 177 - end of helix removed outlier: 3.554A pdb=" N ILE C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP C 181 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 218 through 237 Processing helix chain 'C' and resid 256 through 272 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 296 through 299 No H-bonds generated for 'chain 'C' and resid 296 through 299' Processing helix chain 'C' and resid 311 through 330 Processing helix chain 'C' and resid 336 through 350 removed outlier: 4.533A pdb=" N PHE C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) Proline residue: C 342 - end of helix Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 385 through 401 removed outlier: 4.769A pdb=" N ASN C 389 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 418 Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 436 through 448 Processing helix chain 'C' and resid 457 through 463 Processing helix chain 'C' and resid 470 through 482 Processing helix chain 'C' and resid 488 through 505 removed outlier: 3.803A pdb=" N ASN C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 518 through 530 Processing helix chain 'C' and resid 535 through 545 Processing helix chain 'C' and resid 560 through 565 removed outlier: 4.584A pdb=" N GLY C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'D' and resid 1 through 12 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.774A pdb=" N SER D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 103 through 115 Processing helix chain 'D' and resid 117 through 126 removed outlier: 4.204A pdb=" N VAL D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 152 Processing helix chain 'D' and resid 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 173 through 181 Proline residue: D 177 - end of helix removed outlier: 3.554A pdb=" N ILE D 180 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 181 " --> pdb=" O TRP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 218 through 237 Processing helix chain 'D' and resid 256 through 272 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 296 through 299 No H-bonds generated for 'chain 'D' and resid 296 through 299' Processing helix chain 'D' and resid 311 through 330 Processing helix chain 'D' and resid 336 through 350 removed outlier: 4.532A pdb=" N PHE D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) Proline residue: D 342 - end of helix Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 385 through 401 removed outlier: 4.769A pdb=" N ASN D 389 " --> pdb=" O ARG D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'D' and resid 436 through 448 Processing helix chain 'D' and resid 457 through 463 Processing helix chain 'D' and resid 470 through 482 Processing helix chain 'D' and resid 488 through 505 removed outlier: 3.803A pdb=" N ASN D 505 " --> pdb=" O ASN D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 518 through 530 Processing helix chain 'D' and resid 535 through 545 Processing helix chain 'D' and resid 560 through 565 removed outlier: 4.584A pdb=" N GLY D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'E' and resid 1 through 12 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 58 through 66 removed outlier: 3.774A pdb=" N SER E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 103 through 115 Processing helix chain 'E' and resid 117 through 126 removed outlier: 4.204A pdb=" N VAL E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 152 Processing helix chain 'E' and resid 167 through 170 No H-bonds generated for 'chain 'E' and resid 167 through 170' Processing helix chain 'E' and resid 173 through 181 Proline residue: E 177 - end of helix removed outlier: 3.554A pdb=" N ILE E 180 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP E 181 " --> pdb=" O TRP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 194 through 205 Processing helix chain 'E' and resid 218 through 237 Processing helix chain 'E' and resid 256 through 272 Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 296 through 299 No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 311 through 330 Processing helix chain 'E' and resid 336 through 350 removed outlier: 4.533A pdb=" N PHE E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Proline residue: E 342 - end of helix Processing helix chain 'E' and resid 355 through 363 Processing helix chain 'E' and resid 373 through 383 Processing helix chain 'E' and resid 385 through 401 removed outlier: 4.768A pdb=" N ASN E 389 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 418 Processing helix chain 'E' and resid 420 through 433 Processing helix chain 'E' and resid 436 through 448 Processing helix chain 'E' and resid 457 through 463 Processing helix chain 'E' and resid 470 through 482 Processing helix chain 'E' and resid 488 through 505 removed outlier: 3.803A pdb=" N ASN E 505 " --> pdb=" O ASN E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 514 No H-bonds generated for 'chain 'E' and resid 512 through 514' Processing helix chain 'E' and resid 518 through 530 Processing helix chain 'E' and resid 535 through 545 Processing helix chain 'E' and resid 560 through 565 removed outlier: 4.583A pdb=" N GLY E 565 " --> pdb=" O ASN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 Processing helix chain 'F' and resid 1 through 12 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 58 through 66 removed outlier: 3.774A pdb=" N SER F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 73 Processing helix chain 'F' and resid 103 through 115 Processing helix chain 'F' and resid 117 through 126 removed outlier: 4.204A pdb=" N VAL F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 152 Processing helix chain 'F' and resid 167 through 170 No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 173 through 181 Proline residue: F 177 - end of helix removed outlier: 3.554A pdb=" N ILE F 180 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP F 181 " --> pdb=" O TRP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 218 through 237 Processing helix chain 'F' and resid 256 through 272 Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 296 through 299 No H-bonds generated for 'chain 'F' and resid 296 through 299' Processing helix chain 'F' and resid 311 through 330 Processing helix chain 'F' and resid 336 through 350 removed outlier: 4.533A pdb=" N PHE F 341 " --> pdb=" O ILE F 337 " (cutoff:3.500A) Proline residue: F 342 - end of helix Processing helix chain 'F' and resid 355 through 363 Processing helix chain 'F' and resid 373 through 383 Processing helix chain 'F' and resid 385 through 401 removed outlier: 4.769A pdb=" N ASN F 389 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 418 Processing helix chain 'F' and resid 420 through 433 Processing helix chain 'F' and resid 436 through 448 Processing helix chain 'F' and resid 457 through 463 Processing helix chain 'F' and resid 470 through 482 Processing helix chain 'F' and resid 488 through 505 removed outlier: 3.802A pdb=" N ASN F 505 " --> pdb=" O ASN F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 514 No H-bonds generated for 'chain 'F' and resid 512 through 514' Processing helix chain 'F' and resid 518 through 530 Processing helix chain 'F' and resid 535 through 545 Processing helix chain 'F' and resid 560 through 565 removed outlier: 4.583A pdb=" N GLY F 565 " --> pdb=" O ASN F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 Processing sheet with id= A, first strand: chain 'A' and resid 84 through 89 Processing sheet with id= B, first strand: chain 'A' and resid 283 through 286 Processing sheet with id= C, first strand: chain 'B' and resid 84 through 89 Processing sheet with id= D, first strand: chain 'B' and resid 283 through 286 Processing sheet with id= E, first strand: chain 'C' and resid 84 through 89 Processing sheet with id= F, first strand: chain 'C' and resid 283 through 286 Processing sheet with id= G, first strand: chain 'D' and resid 84 through 89 Processing sheet with id= H, first strand: chain 'D' and resid 283 through 286 Processing sheet with id= I, first strand: chain 'E' and resid 84 through 89 Processing sheet with id= J, first strand: chain 'E' and resid 283 through 286 Processing sheet with id= K, first strand: chain 'F' and resid 84 through 89 Processing sheet with id= L, first strand: chain 'F' and resid 283 through 286 1320 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 7.57 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 5052 1.27 - 1.41: 8787 1.41 - 1.54: 17797 1.54 - 1.67: 338 1.67 - 1.81: 186 Bond restraints: 32160 Sorted by residual: bond pdb=" OH PTR C 44 " pdb=" P PTR C 44 " ideal model delta sigma weight residual 1.769 1.610 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" OH PTR B 44 " pdb=" P PTR B 44 " ideal model delta sigma weight residual 1.769 1.611 0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" OH PTR E 44 " pdb=" P PTR E 44 " ideal model delta sigma weight residual 1.769 1.611 0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" OH PTR D 44 " pdb=" P PTR D 44 " ideal model delta sigma weight residual 1.769 1.611 0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" OH PTR F 44 " pdb=" P PTR F 44 " ideal model delta sigma weight residual 1.769 1.611 0.158 2.00e-02 2.50e+03 6.22e+01 ... (remaining 32155 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.97: 764 106.97 - 113.78: 17133 113.78 - 120.58: 14344 120.58 - 127.39: 11127 127.39 - 134.19: 198 Bond angle restraints: 43566 Sorted by residual: angle pdb=" C TYR A 242 " pdb=" N SER A 243 " pdb=" CA SER A 243 " ideal model delta sigma weight residual 122.72 131.81 -9.09 1.38e+00 5.25e-01 4.34e+01 angle pdb=" C TYR D 242 " pdb=" N SER D 243 " pdb=" CA SER D 243 " ideal model delta sigma weight residual 122.72 131.81 -9.09 1.38e+00 5.25e-01 4.34e+01 angle pdb=" C TYR F 242 " pdb=" N SER F 243 " pdb=" CA SER F 243 " ideal model delta sigma weight residual 122.72 131.80 -9.08 1.38e+00 5.25e-01 4.33e+01 angle pdb=" C TYR E 242 " pdb=" N SER E 243 " pdb=" CA SER E 243 " ideal model delta sigma weight residual 122.72 131.79 -9.07 1.38e+00 5.25e-01 4.32e+01 angle pdb=" C TYR C 242 " pdb=" N SER C 243 " pdb=" CA SER C 243 " ideal model delta sigma weight residual 122.72 131.79 -9.07 1.38e+00 5.25e-01 4.32e+01 ... (remaining 43561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.24: 17043 26.24 - 52.49: 1449 52.49 - 78.73: 366 78.73 - 104.97: 54 104.97 - 131.21: 6 Dihedral angle restraints: 18918 sinusoidal: 8172 harmonic: 10746 Sorted by residual: dihedral pdb=" C ARG B 244 " pdb=" N ARG B 244 " pdb=" CA ARG B 244 " pdb=" CB ARG B 244 " ideal model delta harmonic sigma weight residual -122.60 -134.15 11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C ARG A 244 " pdb=" N ARG A 244 " pdb=" CA ARG A 244 " pdb=" CB ARG A 244 " ideal model delta harmonic sigma weight residual -122.60 -134.11 11.51 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C ARG E 244 " pdb=" N ARG E 244 " pdb=" CA ARG E 244 " pdb=" CB ARG E 244 " ideal model delta harmonic sigma weight residual -122.60 -134.11 11.51 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 18915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4398 0.102 - 0.204: 234 0.204 - 0.306: 6 0.306 - 0.408: 12 0.408 - 0.511: 6 Chirality restraints: 4656 Sorted by residual: chirality pdb=" CA ARG B 244 " pdb=" N ARG B 244 " pdb=" C ARG B 244 " pdb=" CB ARG B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" CA ARG A 244 " pdb=" N ARG A 244 " pdb=" C ARG A 244 " pdb=" CB ARG A 244 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.47e+00 chirality pdb=" CA ARG F 244 " pdb=" N ARG F 244 " pdb=" C ARG F 244 " pdb=" CB ARG F 244 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 4653 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 523 " -0.030 2.00e-02 2.50e+03 3.81e-02 2.54e+01 pdb=" CG PHE F 523 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE F 523 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 523 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE F 523 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE F 523 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE F 523 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 523 " -0.030 2.00e-02 2.50e+03 3.80e-02 2.53e+01 pdb=" CG PHE E 523 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE E 523 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 523 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE E 523 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE E 523 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 523 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 523 " -0.030 2.00e-02 2.50e+03 3.80e-02 2.52e+01 pdb=" CG PHE C 523 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE C 523 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 523 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE C 523 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE C 523 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 523 " -0.002 2.00e-02 2.50e+03 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 859 2.70 - 3.25: 32315 3.25 - 3.80: 55387 3.80 - 4.35: 73443 4.35 - 4.90: 113480 Nonbonded interactions: 275484 Sorted by model distance: nonbonded pdb=" NZ LYS D 530 " pdb=" OE2 GLU D 593 " model vdw 2.153 2.520 nonbonded pdb=" NZ LYS E 530 " pdb=" OE2 GLU E 593 " model vdw 2.154 2.520 nonbonded pdb=" NZ LYS F 530 " pdb=" OE2 GLU F 593 " model vdw 2.154 2.520 nonbonded pdb=" NZ LYS B 530 " pdb=" OE2 GLU B 593 " model vdw 2.154 2.520 nonbonded pdb=" NZ LYS C 530 " pdb=" OE2 GLU C 593 " model vdw 2.154 2.520 ... (remaining 275479 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' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 120 5.16 5 C 20076 2.51 5 N 5028 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.010 Extract box with map and model: 9.680 Check model and map are aligned: 0.340 Process input model: 62.350 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.007 0.159 32160 Z= 0.425 Angle : 0.854 10.138 43566 Z= 0.489 Chirality : 0.058 0.511 4656 Planarity : 0.005 0.041 5364 Dihedral : 20.281 131.214 11970 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.18 % Favored : 98.65 % Rotamer Outliers : 5.53 % Cbeta Deviations : 0.17 % 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: 0.06 (0.13), residues: 3546 helix: 0.67 (0.11), residues: 2130 sheet: -0.34 (0.41), residues: 156 loop : -0.89 (0.17), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 716 time to evaluate : 2.749 Fit side-chains revert: symmetry clash outliers start: 186 outliers final: 8 residues processed: 807 average time/residue: 1.2433 time to fit residues: 1171.7258 Evaluate side-chains 535 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 527 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.3200 time to fit residues: 5.2632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.2980 chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 206 GLN A 311 ASN A 320 ASN A 360 ASN A 366 ASN A 429 HIS A 528 ASN A 543 GLN B 161 HIS B 360 ASN B 429 HIS B 433 ASN B 528 ASN B 543 GLN C 139 ASN C 161 HIS C 264 ASN C 360 ASN C 429 HIS C 433 ASN C 441 GLN C 501 ASN C 528 ASN C 543 GLN C 573 ASN D 67 HIS D 139 ASN D 257 ASN D 264 ASN D 366 ASN D 462 ASN D 528 ASN E 161 HIS E 206 GLN E 311 ASN E 320 ASN E 360 ASN E 366 ASN E 429 HIS E 433 ASN E 543 GLN F 139 ASN F 257 ASN F 366 ASN F 462 ASN F 528 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 32160 Z= 0.210 Angle : 0.545 8.597 43566 Z= 0.306 Chirality : 0.042 0.161 4656 Planarity : 0.004 0.041 5364 Dihedral : 14.312 133.144 4506 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.13 % Favored : 98.70 % Rotamer Outliers : 4.10 % 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: 0.60 (0.14), residues: 3546 helix: 1.12 (0.11), residues: 2130 sheet: -0.29 (0.42), residues: 156 loop : -0.67 (0.17), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 552 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 62 residues processed: 642 average time/residue: 1.1915 time to fit residues: 900.7175 Evaluate side-chains 588 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 526 time to evaluate : 2.753 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 44 residues processed: 18 average time/residue: 0.5594 time to fit residues: 17.4525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 360 ASN A 528 ASN A 543 GLN B 311 ASN B 360 ASN B 501 ASN B 505 ASN B 528 ASN B 543 GLN C 311 ASN C 360 ASN C 528 ASN C 543 GLN D 67 HIS D 257 ASN D 311 ASN D 429 HIS D 462 ASN D 505 ASN D 528 ASN E 139 ASN E 161 HIS E 360 ASN E 497 GLN E 528 ASN E 543 GLN F 67 HIS F 139 ASN F 257 ASN F 311 ASN F 429 HIS F 462 ASN F 501 ASN F 505 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 32160 Z= 0.266 Angle : 0.572 9.627 43566 Z= 0.319 Chirality : 0.044 0.243 4656 Planarity : 0.004 0.043 5364 Dihedral : 14.301 134.944 4506 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.38 % Favored : 98.45 % Rotamer Outliers : 4.10 % 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: 0.59 (0.14), residues: 3546 helix: 1.16 (0.11), residues: 2118 sheet: -0.03 (0.41), residues: 156 loop : -0.80 (0.17), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 526 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 76 residues processed: 615 average time/residue: 1.2262 time to fit residues: 885.3745 Evaluate side-chains 600 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 524 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 50 residues processed: 26 average time/residue: 0.6192 time to fit residues: 25.2152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 0.0570 chunk 156 optimal weight: 0.9980 chunk 219 optimal weight: 0.7980 chunk 328 optimal weight: 4.9990 chunk 347 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 311 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 399 ASN A 528 ASN A 543 GLN B 528 ASN B 543 GLN C 528 ASN C 543 GLN D 67 HIS D 139 ASN D 257 ASN D 462 ASN D 528 ASN E 139 ASN E 399 ASN E 528 ASN E 543 GLN F 67 HIS F 257 ASN F 462 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 32160 Z= 0.147 Angle : 0.457 8.634 43566 Z= 0.257 Chirality : 0.038 0.149 4656 Planarity : 0.003 0.036 5364 Dihedral : 14.124 134.452 4506 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.04 % Favored : 98.79 % Rotamer Outliers : 3.03 % 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: 0.95 (0.14), residues: 3546 helix: 1.43 (0.11), residues: 2130 sheet: 0.09 (0.41), residues: 156 loop : -0.62 (0.17), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 524 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 56 residues processed: 603 average time/residue: 1.2078 time to fit residues: 858.5984 Evaluate side-chains 570 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 514 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 43 residues processed: 13 average time/residue: 0.8060 time to fit residues: 17.0144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 5.9990 chunk 197 optimal weight: 0.0870 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 312 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 543 GLN B 528 ASN B 543 GLN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN D 67 HIS D 257 ASN D 462 ASN D 501 ASN D 528 ASN E 278 ASN E 528 ASN E 543 GLN F 139 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 32160 Z= 0.176 Angle : 0.477 10.471 43566 Z= 0.269 Chirality : 0.039 0.160 4656 Planarity : 0.003 0.038 5364 Dihedral : 14.097 134.735 4506 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.35 % Favored : 98.48 % Rotamer Outliers : 3.33 % 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: 1.00 (0.14), residues: 3546 helix: 1.53 (0.11), residues: 2112 sheet: 0.07 (0.41), residues: 156 loop : -0.68 (0.17), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 519 time to evaluate : 2.821 Fit side-chains revert: symmetry clash outliers start: 112 outliers final: 61 residues processed: 597 average time/residue: 1.1876 time to fit residues: 835.3178 Evaluate side-chains 566 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 505 time to evaluate : 2.779 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 48 residues processed: 13 average time/residue: 0.4838 time to fit residues: 12.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 528 ASN A 543 GLN B 528 ASN B 543 GLN B 573 ASN C 528 ASN D 139 ASN D 257 ASN D 462 ASN D 528 ASN D 573 ASN E 139 ASN E 543 GLN F 139 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 32160 Z= 0.221 Angle : 0.506 9.602 43566 Z= 0.286 Chirality : 0.041 0.194 4656 Planarity : 0.003 0.040 5364 Dihedral : 14.116 134.904 4506 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.35 % Favored : 98.48 % Rotamer Outliers : 3.77 % 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: 0.97 (0.14), residues: 3546 helix: 1.48 (0.11), residues: 2100 sheet: 0.05 (0.41), residues: 156 loop : -0.62 (0.17), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 509 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 75 residues processed: 597 average time/residue: 1.2480 time to fit residues: 875.3335 Evaluate side-chains 581 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 506 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 58 residues processed: 17 average time/residue: 0.6323 time to fit residues: 18.0569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 197 optimal weight: 0.2980 chunk 293 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 346 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 543 GLN B 543 GLN C 505 ASN C 528 ASN D 139 ASN D 257 ASN D 462 ASN E 528 ASN E 543 GLN F 67 HIS F 139 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 32160 Z= 0.178 Angle : 0.472 8.986 43566 Z= 0.268 Chirality : 0.039 0.164 4656 Planarity : 0.003 0.042 5364 Dihedral : 14.049 134.364 4506 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.41 % Favored : 98.42 % Rotamer Outliers : 2.94 % 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: 1.04 (0.14), residues: 3546 helix: 1.52 (0.11), residues: 2106 sheet: -0.00 (0.41), residues: 156 loop : -0.56 (0.17), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 507 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 71 residues processed: 587 average time/residue: 1.2383 time to fit residues: 857.9595 Evaluate side-chains 581 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 510 time to evaluate : 2.782 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 63 residues processed: 8 average time/residue: 0.4989 time to fit residues: 9.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN C 419 ASN D 139 ASN D 257 ASN D 462 ASN E 528 ASN E 543 GLN F 139 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 32160 Z= 0.209 Angle : 0.496 8.717 43566 Z= 0.281 Chirality : 0.041 0.180 4656 Planarity : 0.004 0.060 5364 Dihedral : 14.062 134.380 4506 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.41 % Favored : 98.42 % Rotamer Outliers : 3.12 % 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: 0.95 (0.14), residues: 3546 helix: 1.47 (0.11), residues: 2112 sheet: -0.00 (0.41), residues: 156 loop : -0.65 (0.17), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 518 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 76 residues processed: 598 average time/residue: 1.2066 time to fit residues: 847.7018 Evaluate side-chains 588 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 512 time to evaluate : 2.758 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 67 residues processed: 9 average time/residue: 0.4507 time to fit residues: 9.6443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 323 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN D 139 ASN D 257 ASN D 462 ASN E 543 GLN F 139 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 32160 Z= 0.208 Angle : 0.497 8.371 43566 Z= 0.281 Chirality : 0.041 0.180 4656 Planarity : 0.003 0.048 5364 Dihedral : 14.048 134.121 4506 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.41 % Favored : 98.42 % Rotamer Outliers : 3.09 % 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: 1.00 (0.14), residues: 3546 helix: 1.49 (0.11), residues: 2100 sheet: -0.02 (0.41), residues: 156 loop : -0.59 (0.17), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 514 time to evaluate : 2.848 Fit side-chains revert: symmetry clash outliers start: 104 outliers final: 77 residues processed: 596 average time/residue: 1.2235 time to fit residues: 863.2383 Evaluate side-chains 589 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 512 time to evaluate : 2.777 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 67 residues processed: 10 average time/residue: 0.4434 time to fit residues: 10.3938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 2.9990 chunk 341 optimal weight: 0.0020 chunk 208 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 543 GLN B 543 GLN C 543 GLN D 139 ASN D 257 ASN D 462 ASN D 543 GLN E 543 GLN F 139 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 32160 Z= 0.176 Angle : 0.471 8.076 43566 Z= 0.266 Chirality : 0.039 0.160 4656 Planarity : 0.003 0.040 5364 Dihedral : 13.982 133.463 4506 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.35 % Favored : 98.48 % Rotamer Outliers : 2.64 % 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: 1.09 (0.14), residues: 3546 helix: 1.56 (0.11), residues: 2106 sheet: -0.07 (0.41), residues: 156 loop : -0.52 (0.17), residues: 1284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 513 time to evaluate : 2.981 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 74 residues processed: 590 average time/residue: 1.2452 time to fit residues: 861.9501 Evaluate side-chains 588 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 514 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 67 residues processed: 7 average time/residue: 0.5007 time to fit residues: 8.6947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 9.9990 chunk 304 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN B 360 ASN B 419 ASN B 543 GLN C 360 ASN C 399 ASN C 543 GLN D 139 ASN D 161 HIS D 257 ASN D 419 ASN D 462 ASN E 230 HIS E 360 ASN E 505 ASN E 543 GLN F 139 ASN F 196 ASN F 257 ASN F 419 ASN F 462 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.159557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135815 restraints weight = 24984.617| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.87 r_work: 0.3251 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.110 32160 Z= 0.477 Angle : 0.715 8.769 43566 Z= 0.399 Chirality : 0.054 0.302 4656 Planarity : 0.005 0.097 5364 Dihedral : 14.271 136.114 4506 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.55 % Favored : 98.28 % Rotamer Outliers : 3.00 % 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: 0.51 (0.14), residues: 3546 helix: 1.05 (0.11), residues: 2100 sheet: 0.09 (0.40), residues: 156 loop : -0.73 (0.17), residues: 1290 =============================================================================== Job complete usr+sys time: 12216.49 seconds wall clock time: 212 minutes 46.15 seconds (12766.15 seconds total)