Starting phenix.real_space_refine on Wed Jun 26 06:54:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/06_2024/7r06_14220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/06_2024/7r06_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_14220/06_2024/7r06_14220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/06_2024/7r06_14220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/06_2024/7r06_14220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r06_14220/06_2024/7r06_14220_updated.pdb" } resolution = 2.27 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= 0.006 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 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. 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-5370/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: 23 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: 23 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: 23 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: 23 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: 23 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: 23 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: 12.46, 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: 10.02 Conformation dependent library (CDL) restraints added in 4.1 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: 10.65 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: 8.35 Time building geometry restraints manager: 11.03 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: 17061 26.24 - 52.49: 1464 52.49 - 78.73: 387 78.73 - 104.97: 54 104.97 - 131.21: 6 Dihedral angle restraints: 18972 sinusoidal: 8226 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 18969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4392 0.102 - 0.204: 240 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.010 Extract box with map and model: 7.760 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 68.790 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.858 10.138 43566 Z= 0.490 Chirality : 0.058 0.511 4656 Planarity : 0.005 0.041 5364 Dihedral : 20.476 131.214 12024 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 % Allowed : 19.88 % Favored : 74.60 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 518 HIS 0.026 0.005 HIS E 429 PHE 0.085 0.008 PHE F 523 TYR 0.061 0.005 TYR F 415 ARG 0.022 0.003 ARG C 521 *********************** 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 : 2.652 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7716 (mmpt) REVERT: A 37 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7691 (pttm) REVERT: A 370 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7644 (t0) REVERT: A 583 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6677 (tm-30) REVERT: B 29 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7605 (mmtm) REVERT: B 446 MET cc_start: 0.8826 (mtp) cc_final: 0.8273 (mtm) REVERT: C 283 LYS cc_start: 0.8681 (pttm) cc_final: 0.8407 (pttm) REVERT: C 316 LYS cc_start: 0.8386 (tmmm) cc_final: 0.8146 (tmmt) REVERT: C 432 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7835 (mtmt) REVERT: C 446 MET cc_start: 0.8794 (mtp) cc_final: 0.8246 (mtm) REVERT: D 280 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.7120 (m-40) REVERT: E 29 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7742 (mmpt) REVERT: E 37 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7655 (pttm) REVERT: E 316 LYS cc_start: 0.8423 (tmmm) cc_final: 0.8214 (tptt) REVERT: E 583 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6738 (tm-30) outliers start: 186 outliers final: 8 residues processed: 807 average time/residue: 1.2049 time to fit residues: 1137.1241 Evaluate side-chains 541 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 526 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 497 GLN Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 497 GLN Chi-restraints excluded: chain E residue 536 LYS Chi-restraints excluded: chain F residue 497 GLN 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: 0.7980 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: 1.2184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 366 ASN A 429 HIS A 528 ASN A 543 GLN B 161 HIS B 311 ASN B 360 ASN B 429 HIS B 433 ASN B 441 GLN B 528 ASN B 543 GLN C 139 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 360 ASN E 366 ASN E 429 HIS E 433 ASN E 543 GLN F 139 ASN F 257 ASN F 366 ASN ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 ASN F 528 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32160 Z= 0.205 Angle : 0.541 8.097 43566 Z= 0.303 Chirality : 0.042 0.162 4656 Planarity : 0.004 0.042 5364 Dihedral : 15.270 133.010 4607 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.07 % Favored : 98.76 % Rotamer: Outliers : 4.04 % Allowed : 19.64 % Favored : 76.32 % 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: 0.62 (0.14), residues: 3546 helix: 1.14 (0.11), residues: 2130 sheet: -0.29 (0.42), residues: 156 loop : -0.65 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 518 HIS 0.020 0.002 HIS D 429 PHE 0.041 0.003 PHE F 299 TYR 0.037 0.003 TYR B 415 ARG 0.008 0.001 ARG D 244 *********************** 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 685 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 549 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8202 (mtpm) cc_final: 0.7787 (mmpt) REVERT: A 32 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7665 (mtpt) REVERT: A 82 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: A 530 LYS cc_start: 0.6984 (ptmt) cc_final: 0.6553 (pttp) REVERT: B 40 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.5921 (mt) REVERT: B 122 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: B 281 LYS cc_start: 0.7944 (mttt) cc_final: 0.7731 (mtpt) REVERT: B 446 MET cc_start: 0.8769 (mtp) cc_final: 0.8134 (mtm) REVERT: C 122 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: C 209 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6908 (mm-30) REVERT: C 281 LYS cc_start: 0.7807 (mttt) cc_final: 0.7563 (mtpt) REVERT: C 283 LYS cc_start: 0.8600 (pttm) cc_final: 0.8385 (pttm) REVERT: C 316 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8129 (ttmt) REVERT: C 324 TYR cc_start: 0.8713 (t80) cc_final: 0.8493 (t80) REVERT: E 29 LYS cc_start: 0.8202 (mtpm) cc_final: 0.7690 (mmpt) REVERT: E 32 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7643 (mtpt) REVERT: E 79 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8053 (tt) REVERT: E 82 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: E 370 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7741 (t0) REVERT: F 82 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: F 158 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8405 (mttt) outliers start: 136 outliers final: 58 residues processed: 634 average time/residue: 1.1701 time to fit residues: 872.2657 Evaluate side-chains 596 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 525 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 465 ASP Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 484 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 291 optimal weight: 0.6980 chunk 324 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 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 139 ASN A 320 ASN A 360 ASN A 528 ASN A 543 GLN B 360 ASN B 501 ASN B 528 ASN B 543 GLN C 161 HIS C 311 ASN C 360 ASN C 528 ASN D 67 HIS D 257 ASN D 311 ASN D 462 ASN D 528 ASN E 139 ASN E 161 HIS E 360 ASN E 399 ASN E 497 GLN E 528 ASN E 543 GLN F 67 HIS F 257 ASN F 311 ASN F 462 ASN F 501 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32160 Z= 0.210 Angle : 0.521 10.186 43566 Z= 0.290 Chirality : 0.042 0.175 4656 Planarity : 0.004 0.041 5364 Dihedral : 14.925 133.654 4560 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.07 % Favored : 98.76 % Rotamer: Outliers : 3.74 % Allowed : 19.67 % Favored : 76.59 % 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: 0.76 (0.14), residues: 3546 helix: 1.24 (0.11), residues: 2130 sheet: -0.02 (0.41), residues: 156 loop : -0.62 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 518 HIS 0.014 0.002 HIS D 429 PHE 0.031 0.003 PHE B 73 TYR 0.023 0.002 TYR C 415 ARG 0.005 0.001 ARG F 244 *********************** 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 652 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 526 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8206 (mtpm) cc_final: 0.7799 (mmpt) REVERT: A 82 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: A 530 LYS cc_start: 0.6829 (ptmt) cc_final: 0.6473 (pttp) REVERT: B 40 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.5944 (mt) REVERT: B 122 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: B 281 LYS cc_start: 0.8007 (mttt) cc_final: 0.7772 (mtpt) REVERT: B 432 LYS cc_start: 0.8244 (mmtm) cc_final: 0.8015 (mptp) REVERT: C 25 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: C 122 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: C 209 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: C 281 LYS cc_start: 0.7965 (mttt) cc_final: 0.7705 (mtpt) REVERT: C 316 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8081 (ttmt) REVERT: C 324 TYR cc_start: 0.8739 (t80) cc_final: 0.8495 (t80) REVERT: D 453 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6282 (m-30) REVERT: E 1 MET cc_start: 0.7296 (ttm) cc_final: 0.7003 (ttp) REVERT: E 29 LYS cc_start: 0.8226 (mtpm) cc_final: 0.7711 (mmpt) REVERT: E 79 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8077 (tt) REVERT: E 82 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: E 370 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7644 (t0) REVERT: F 82 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: F 158 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8400 (mttt) REVERT: F 280 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.7144 (m-40) REVERT: F 432 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7863 (mtmt) outliers start: 126 outliers final: 66 residues processed: 612 average time/residue: 1.1887 time to fit residues: 854.7643 Evaluate side-chains 603 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 523 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 465 ASP Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 300 SER Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 505 ASN B 528 ASN B 543 GLN C 528 ASN D 67 HIS D 139 ASN D 257 ASN D 429 HIS D 462 ASN D 501 ASN D 505 ASN D 528 ASN E 139 ASN E 528 ASN E 543 GLN F 67 HIS F 139 ASN F 257 ASN F 429 HIS F 462 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32160 Z= 0.204 Angle : 0.513 10.234 43566 Z= 0.285 Chirality : 0.041 0.181 4656 Planarity : 0.003 0.040 5364 Dihedral : 14.835 133.577 4560 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.33 % Favored : 98.51 % Rotamer: Outliers : 3.59 % Allowed : 19.67 % Favored : 76.74 % 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: 0.84 (0.14), residues: 3546 helix: 1.39 (0.11), residues: 2112 sheet: 0.07 (0.41), residues: 156 loop : -0.74 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 518 HIS 0.012 0.002 HIS D 429 PHE 0.025 0.002 PHE E 73 TYR 0.016 0.002 TYR C 415 ARG 0.005 0.001 ARG F 244 *********************** 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 647 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 526 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8194 (mtpm) cc_final: 0.7812 (mmpt) REVERT: A 82 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: A 370 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7596 (t0) REVERT: A 530 LYS cc_start: 0.6839 (ptmt) cc_final: 0.6390 (pttp) REVERT: B 25 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: B 40 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5797 (mt) REVERT: B 122 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: B 281 LYS cc_start: 0.8013 (mttt) cc_final: 0.7780 (mtpt) REVERT: C 25 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: C 122 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: C 209 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: C 281 LYS cc_start: 0.7949 (mttt) cc_final: 0.7710 (mtpt) REVERT: C 283 LYS cc_start: 0.8578 (pttm) cc_final: 0.8372 (pttm) REVERT: C 316 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8088 (ttmt) REVERT: C 324 TYR cc_start: 0.8719 (t80) cc_final: 0.8501 (t80) REVERT: C 536 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6910 (tptp) REVERT: D 370 ASN cc_start: 0.8085 (m-40) cc_final: 0.7611 (t0) REVERT: D 452 ASP cc_start: 0.7992 (p0) cc_final: 0.7761 (p0) REVERT: D 453 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6241 (m-30) REVERT: E 29 LYS cc_start: 0.8206 (mtpm) cc_final: 0.7800 (mmpt) REVERT: E 79 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8100 (tt) REVERT: E 82 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: E 370 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7652 (t0) REVERT: F 40 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6050 (mt) REVERT: F 82 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: F 122 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: F 158 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8437 (mttt) REVERT: F 280 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7142 (m-40) REVERT: F 432 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7883 (mtmt) REVERT: F 452 ASP cc_start: 0.7906 (p0) cc_final: 0.7699 (p0) outliers start: 121 outliers final: 67 residues processed: 602 average time/residue: 1.1874 time to fit residues: 839.1993 Evaluate side-chains 603 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 517 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 465 ASP Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 300 SER Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 312 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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 419 ASN B 528 ASN B 543 GLN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 419 ASN C 505 ASN C 528 ASN D 139 ASN D 257 ASN D 462 ASN D 528 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN E 360 ASN E 528 ASN E 543 GLN F 139 ASN F 257 ASN F 462 ASN F 505 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32160 Z= 0.291 Angle : 0.582 11.498 43566 Z= 0.323 Chirality : 0.045 0.257 4656 Planarity : 0.004 0.044 5364 Dihedral : 14.891 134.553 4560 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.49 % Favored : 98.34 % Rotamer: Outliers : 4.72 % Allowed : 18.42 % Favored : 76.86 % 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: 0.70 (0.14), residues: 3546 helix: 1.23 (0.11), residues: 2118 sheet: 0.11 (0.41), residues: 156 loop : -0.73 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 518 HIS 0.009 0.002 HIS B 161 PHE 0.026 0.003 PHE E 73 TYR 0.019 0.003 TYR A 324 ARG 0.005 0.001 ARG D 244 *********************** 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 676 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 517 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: A 370 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7757 (t0) REVERT: A 494 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8483 (mptp) REVERT: A 530 LYS cc_start: 0.6845 (ptmt) cc_final: 0.6377 (pttp) REVERT: B 65 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7294 (mtm180) REVERT: B 122 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: B 280 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7045 (m110) REVERT: B 281 LYS cc_start: 0.7972 (mttt) cc_final: 0.7731 (mtpt) REVERT: C 65 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7307 (mtm180) REVERT: C 122 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: C 209 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: C 281 LYS cc_start: 0.7912 (mttt) cc_final: 0.7649 (mtpt) REVERT: C 324 TYR cc_start: 0.8747 (t80) cc_final: 0.8524 (t80) REVERT: C 536 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7014 (tptp) REVERT: D 10 ASP cc_start: 0.7682 (m-30) cc_final: 0.7482 (m-30) REVERT: D 40 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6105 (mt) REVERT: D 65 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8139 (mtm180) REVERT: D 82 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: D 122 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: D 370 ASN cc_start: 0.8176 (m-40) cc_final: 0.7697 (t0) REVERT: D 452 ASP cc_start: 0.8006 (p0) cc_final: 0.7777 (p0) REVERT: E 29 LYS cc_start: 0.8222 (mtpm) cc_final: 0.7819 (mmpt) REVERT: E 79 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8172 (tt) REVERT: E 82 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: E 370 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7778 (t0) REVERT: E 545 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: F 40 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6155 (mt) REVERT: F 65 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8133 (mtm180) REVERT: F 82 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: F 122 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: F 158 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8465 (mttt) REVERT: F 280 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7200 (m-40) REVERT: F 432 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7930 (mtmt) REVERT: F 452 ASP cc_start: 0.7942 (p0) cc_final: 0.7726 (p0) outliers start: 159 outliers final: 78 residues processed: 623 average time/residue: 1.2297 time to fit residues: 895.3618 Evaluate side-chains 609 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 507 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 465 ASP Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 545 GLN Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.9990 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: 0.9980 chunk 115 optimal weight: 0.3980 chunk 182 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 543 GLN B 573 ASN C 528 ASN D 139 ASN D 257 ASN D 462 ASN D 528 ASN E 139 ASN E 528 ASN E 543 GLN F 67 HIS F 139 ASN F 161 HIS F 257 ASN F 462 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32160 Z= 0.234 Angle : 0.534 11.249 43566 Z= 0.296 Chirality : 0.043 0.222 4656 Planarity : 0.004 0.042 5364 Dihedral : 14.809 133.906 4560 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.18 % Favored : 98.65 % Rotamer: Outliers : 4.58 % Allowed : 18.27 % Favored : 77.15 % 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: 0.78 (0.14), residues: 3546 helix: 1.33 (0.11), residues: 2112 sheet: 0.14 (0.41), residues: 156 loop : -0.75 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 518 HIS 0.006 0.001 HIS B 161 PHE 0.020 0.002 PHE E 73 TYR 0.018 0.002 TYR F 324 ARG 0.004 0.001 ARG E 65 *********************** 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 667 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 513 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: A 370 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7724 (t0) REVERT: A 494 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8442 (mptp) REVERT: A 530 LYS cc_start: 0.6842 (ptmt) cc_final: 0.6480 (pttp) REVERT: A 536 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7401 (tptt) REVERT: B 65 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7283 (mtm180) REVERT: B 122 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: B 281 LYS cc_start: 0.8040 (mttt) cc_final: 0.7801 (mtpt) REVERT: B 303 GLU cc_start: 0.6698 (pt0) cc_final: 0.6338 (pm20) REVERT: C 65 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7295 (mtm180) REVERT: C 122 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: C 209 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.7007 (mm-30) REVERT: C 281 LYS cc_start: 0.7958 (mttt) cc_final: 0.7714 (mtpt) REVERT: C 316 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (ttmt) REVERT: C 324 TYR cc_start: 0.8723 (t80) cc_final: 0.8497 (t80) REVERT: C 450 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6989 (mp0) REVERT: C 536 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7012 (tptp) REVERT: D 1 MET cc_start: 0.7253 (ttt) cc_final: 0.7012 (ttm) REVERT: D 10 ASP cc_start: 0.7739 (m-30) cc_final: 0.7504 (m-30) REVERT: D 40 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.5962 (mt) REVERT: D 65 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8112 (mtm180) REVERT: D 82 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: D 122 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: D 370 ASN cc_start: 0.8118 (m-40) cc_final: 0.7658 (t0) REVERT: D 452 ASP cc_start: 0.7979 (p0) cc_final: 0.7745 (p0) REVERT: D 487 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7848 (mmpt) REVERT: E 79 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8068 (tt) REVERT: E 82 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: E 370 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7741 (t0) REVERT: E 545 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: F 40 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.5959 (mt) REVERT: F 65 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8114 (mtm180) REVERT: F 82 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: F 122 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: F 158 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8442 (mttt) REVERT: F 265 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: F 370 ASN cc_start: 0.8120 (m-40) cc_final: 0.7571 (t0) REVERT: F 432 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7876 (mtmt) REVERT: F 452 ASP cc_start: 0.8010 (p0) cc_final: 0.7787 (p0) REVERT: F 453 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6441 (m-30) outliers start: 154 outliers final: 83 residues processed: 615 average time/residue: 1.1768 time to fit residues: 849.6772 Evaluate side-chains 618 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 509 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 465 ASP Chi-restraints excluded: chain E residue 545 GLN Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 453 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 198 optimal weight: 0.0060 chunk 254 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 346 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 211 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 543 GLN D 67 HIS D 139 ASN D 257 ASN D 462 ASN E 139 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32160 Z= 0.145 Angle : 0.450 10.215 43566 Z= 0.250 Chirality : 0.038 0.148 4656 Planarity : 0.003 0.038 5364 Dihedral : 14.616 132.364 4560 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.24 % Favored : 98.59 % Rotamer: Outliers : 2.97 % Allowed : 20.02 % Favored : 77.01 % 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: 0.99 (0.14), residues: 3546 helix: 1.42 (0.11), residues: 2166 sheet: 0.05 (0.41), residues: 156 loop : -0.58 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 585 HIS 0.003 0.001 HIS F 67 PHE 0.012 0.001 PHE F 231 TYR 0.015 0.001 TYR B 227 ARG 0.004 0.000 ARG F 244 *********************** 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 627 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 527 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7544 (mtpt) REVERT: A 82 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8102 (t0) REVERT: A 157 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8044 (tp) REVERT: A 530 LYS cc_start: 0.6781 (ptmt) cc_final: 0.6409 (pttp) REVERT: B 122 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: B 281 LYS cc_start: 0.7955 (mttt) cc_final: 0.7735 (mtpt) REVERT: B 450 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7031 (mp0) REVERT: C 25 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: C 122 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: C 209 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: C 265 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: C 281 LYS cc_start: 0.7798 (mttt) cc_final: 0.7589 (mtpt) REVERT: C 316 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (ttmt) REVERT: C 324 TYR cc_start: 0.8642 (t80) cc_final: 0.8426 (t80) REVERT: C 432 LYS cc_start: 0.8043 (mptp) cc_final: 0.7699 (mtmt) REVERT: C 450 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6995 (mp0) REVERT: C 536 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6955 (tptp) REVERT: D 10 ASP cc_start: 0.7753 (m-30) cc_final: 0.7495 (m-30) REVERT: D 40 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5602 (mt) REVERT: D 452 ASP cc_start: 0.7884 (p0) cc_final: 0.7671 (p0) REVERT: D 487 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7868 (mmpt) REVERT: E 79 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7972 (tt) REVERT: E 82 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8114 (t0) REVERT: E 370 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7611 (t0) REVERT: F 40 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5661 (mt) REVERT: F 122 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: F 265 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: F 432 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7750 (mtmt) REVERT: F 452 ASP cc_start: 0.7940 (p0) cc_final: 0.7713 (p0) REVERT: F 453 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6436 (m-30) outliers start: 100 outliers final: 55 residues processed: 597 average time/residue: 1.2022 time to fit residues: 843.0101 Evaluate side-chains 586 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 513 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 516 LYS Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 453 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 207 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 220 optimal weight: 0.0270 chunk 236 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 399 ASN B 543 GLN C 399 ASN C 543 GLN D 139 ASN D 257 ASN D 399 ASN D 462 ASN D 543 GLN E 139 ASN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 462 ASN E 528 ASN E 543 GLN F 139 ASN F 257 ASN F 399 ASN F 462 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 32160 Z= 0.148 Angle : 0.448 9.440 43566 Z= 0.249 Chirality : 0.038 0.143 4656 Planarity : 0.003 0.037 5364 Dihedral : 14.521 132.219 4560 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.21 % Favored : 98.62 % Rotamer: Outliers : 2.82 % Allowed : 20.44 % Favored : 76.74 % 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: 1.10 (0.14), residues: 3546 helix: 1.52 (0.11), residues: 2160 sheet: 0.05 (0.41), residues: 156 loop : -0.54 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 585 HIS 0.003 0.001 HIS F 169 PHE 0.013 0.001 PHE D 231 TYR 0.027 0.001 TYR C 142 ARG 0.004 0.000 ARG F 244 *********************** 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 622 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 527 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7913 (tp) REVERT: A 370 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7594 (t0) REVERT: A 487 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7819 (pmtt) REVERT: A 530 LYS cc_start: 0.6706 (ptmt) cc_final: 0.6440 (mmtt) REVERT: B 25 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: B 122 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: B 450 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7020 (mp0) REVERT: C 25 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: C 122 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: C 209 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6854 (mm-30) REVERT: C 281 LYS cc_start: 0.7823 (mttt) cc_final: 0.7621 (mtpt) REVERT: C 316 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8067 (ttmt) REVERT: C 450 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7012 (mp0) REVERT: C 536 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6944 (tptp) REVERT: D 10 ASP cc_start: 0.7739 (m-30) cc_final: 0.7452 (m-30) REVERT: D 40 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5456 (mt) REVERT: D 65 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8036 (mtm180) REVERT: D 122 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: D 452 ASP cc_start: 0.7894 (p0) cc_final: 0.7659 (p0) REVERT: D 453 ASP cc_start: 0.6529 (OUTLIER) cc_final: 0.6167 (m-30) REVERT: D 487 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7877 (mmpt) REVERT: E 79 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8050 (tt) REVERT: E 370 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7629 (t0) REVERT: E 487 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7764 (pmtt) REVERT: F 40 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5402 (mt) REVERT: F 452 ASP cc_start: 0.7937 (p0) cc_final: 0.7704 (p0) REVERT: F 453 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6454 (m-30) outliers start: 95 outliers final: 50 residues processed: 591 average time/residue: 1.1873 time to fit residues: 825.6834 Evaluate side-chains 578 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 511 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 516 LYS Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 453 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 323 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 322 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 278 ASN A 399 ASN A 462 ASN A 543 GLN B 462 ASN B 543 GLN C 360 ASN C 462 ASN C 543 GLN D 139 ASN D 257 ASN D 462 ASN D 543 GLN E 139 ASN E 320 ASN E 462 ASN E 528 ASN E 543 GLN F 139 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32160 Z= 0.201 Angle : 0.495 8.653 43566 Z= 0.276 Chirality : 0.040 0.166 4656 Planarity : 0.003 0.040 5364 Dihedral : 14.535 132.584 4560 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.38 % Favored : 98.45 % Rotamer: Outliers : 2.82 % Allowed : 20.77 % Favored : 76.41 % 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: 1.10 (0.14), residues: 3546 helix: 1.58 (0.11), residues: 2100 sheet: -0.02 (0.41), residues: 156 loop : -0.53 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 518 HIS 0.005 0.001 HIS D 169 PHE 0.017 0.002 PHE F 231 TYR 0.021 0.002 TYR C 324 ARG 0.006 0.001 ARG E 431 *********************** 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 616 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 521 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7632 (t0) REVERT: A 487 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7812 (pmtt) REVERT: A 494 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8394 (mptp) REVERT: A 530 LYS cc_start: 0.6771 (ptmt) cc_final: 0.6404 (pttp) REVERT: B 122 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: B 265 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: B 432 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7856 (mttp) REVERT: B 450 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7032 (mp0) REVERT: C 25 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: C 122 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: C 209 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: C 281 LYS cc_start: 0.7798 (mttt) cc_final: 0.7578 (mtpt) REVERT: C 316 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8119 (ttmt) REVERT: C 536 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6979 (tptp) REVERT: D 10 ASP cc_start: 0.7774 (m-30) cc_final: 0.7473 (m-30) REVERT: D 65 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8069 (mtm180) REVERT: D 122 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: D 452 ASP cc_start: 0.7924 (p0) cc_final: 0.7682 (p0) REVERT: E 79 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8096 (tt) REVERT: E 370 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7686 (t0) REVERT: E 487 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7763 (pmtt) REVERT: E 583 GLU cc_start: 0.7706 (mm-30) cc_final: 0.6853 (tm-30) REVERT: F 40 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5437 (mt) REVERT: F 65 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8068 (mtm180) REVERT: F 452 ASP cc_start: 0.7959 (p0) cc_final: 0.7723 (p0) REVERT: F 453 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6452 (m-30) outliers start: 95 outliers final: 57 residues processed: 586 average time/residue: 1.1842 time to fit residues: 813.8894 Evaluate side-chains 599 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 525 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 453 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.6980 chunk 341 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 358 optimal weight: 7.9990 chunk 330 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 462 ASN A 528 ASN A 543 GLN B 462 ASN B 543 GLN C 360 ASN C 543 GLN D 139 ASN D 257 ASN D 462 ASN E 360 ASN E 462 ASN E 505 ASN E 543 GLN F 139 ASN F 196 ASN F 257 ASN F 462 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.004 0.083 32160 Z= 0.269 Angle : 0.556 8.313 43566 Z= 0.310 Chirality : 0.044 0.237 4656 Planarity : 0.004 0.043 5364 Dihedral : 14.614 133.904 4560 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.55 % Favored : 98.28 % Rotamer: Outliers : 2.82 % Allowed : 20.74 % Favored : 76.44 % 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: 0.93 (0.14), residues: 3546 helix: 1.41 (0.11), residues: 2100 sheet: 0.05 (0.40), residues: 156 loop : -0.58 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 518 HIS 0.008 0.001 HIS F 169 PHE 0.021 0.003 PHE E 73 TYR 0.023 0.002 TYR A 324 ARG 0.007 0.001 ARG E 431 ********************** 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 616 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 521 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7679 (t0) REVERT: A 487 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7804 (pmtt) REVERT: A 494 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8481 (mptp) REVERT: A 530 LYS cc_start: 0.6820 (ptmt) cc_final: 0.6423 (mmtt) REVERT: B 65 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7287 (mtm180) REVERT: B 122 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: B 432 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7872 (mttp) REVERT: B 450 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7054 (mp0) REVERT: C 122 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: C 209 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: C 281 LYS cc_start: 0.7867 (mttt) cc_final: 0.7639 (mtpt) REVERT: C 432 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7825 (mttp) REVERT: C 536 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7028 (tptp) REVERT: D 10 ASP cc_start: 0.7791 (m-30) cc_final: 0.7482 (m-30) REVERT: D 65 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8103 (mtm180) REVERT: D 82 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: D 122 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6040 (mp0) REVERT: D 452 ASP cc_start: 0.7932 (p0) cc_final: 0.7690 (p0) REVERT: E 79 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8174 (tt) REVERT: E 370 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7741 (t0) REVERT: F 65 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8058 (mtm180) REVERT: F 82 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: F 452 ASP cc_start: 0.7995 (p0) cc_final: 0.7760 (p0) REVERT: F 453 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6364 (m-30) REVERT: F 593 GLU cc_start: 0.6821 (tp30) cc_final: 0.6373 (mm-30) outliers start: 95 outliers final: 65 residues processed: 583 average time/residue: 1.2191 time to fit residues: 834.5013 Evaluate side-chains 593 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 511 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 516 LYS Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 453 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 10.0000 chunk 304 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 462 ASN A 528 ASN A 543 GLN B 360 ASN B 543 GLN C 360 ASN C 543 GLN D 139 ASN D 257 ASN D 419 ASN D 462 ASN E 360 ASN E 462 ASN E 543 GLN F 139 ASN F 257 ASN F 419 ASN F 462 ASN F 535 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.161386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.137694 restraints weight = 24888.073| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.87 r_work: 0.3276 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 32160 Z= 0.308 Angle : 0.592 7.936 43566 Z= 0.329 Chirality : 0.045 0.250 4656 Planarity : 0.004 0.045 5364 Dihedral : 14.675 134.415 4560 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.72 % Favored : 98.11 % Rotamer: Outliers : 3.15 % Allowed : 20.17 % Favored : 76.68 % 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: 0.78 (0.14), residues: 3546 helix: 1.29 (0.11), residues: 2100 sheet: 0.14 (0.40), residues: 156 loop : -0.65 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 518 HIS 0.010 0.002 HIS D 169 PHE 0.023 0.003 PHE C 73 TYR 0.018 0.003 TYR B 227 ARG 0.008 0.001 ARG A 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12117.83 seconds wall clock time: 210 minutes 9.09 seconds (12609.09 seconds total)