Starting phenix.real_space_refine on Fri Mar 15 12:47:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvc_34123/03_2024/7yvc_34123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvc_34123/03_2024/7yvc_34123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvc_34123/03_2024/7yvc_34123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvc_34123/03_2024/7yvc_34123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvc_34123/03_2024/7yvc_34123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvc_34123/03_2024/7yvc_34123.pdb" } resolution = 3.0 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 78 5.16 5 C 7380 2.51 5 N 1935 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C ARG 543": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11662 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "C" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.84, per 1000 atoms: 0.67 Number of scatterers: 11662 At special positions: 0 Unit cell: (110.2, 117.16, 136.88, 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) Ca 1 19.99 S 78 16.00 O 2268 8.00 N 1935 7.00 C 7380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 233 " distance=2.04 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 233 " distance=2.04 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 217 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 431 " distance=2.04 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 363 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 233 " distance=2.04 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 217 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 431 " distance=2.04 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 411 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 381 " distance=2.03 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 Atom "HETATM11477 O5 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM11603 O5 NAG A 702 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 701 " - " ASN A 401 " " NAG A 702 " - " ASN A 377 " " NAG B 701 " - " ASN B 377 " " NAG B 702 " - " ASN B 401 " " NAG C 701 " - " ASN C 377 " " NAG C 702 " - " ASN C 401 " " NAG D 1 " - " ASN A 393 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 169 " " NAG G 1 " - " ASN A 221 " " NAG H 1 " - " ASN B 393 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN B 221 " " NAG L 1 " - " ASN C 393 " " NAG M 1 " - " ASN C 331 " " NAG N 1 " - " ASN C 169 " " NAG O 1 " - " ASN C 221 " Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.1 seconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 44.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 91 through 118 removed outlier: 3.584A pdb=" N TRP A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.010A pdb=" N LYS A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.697A pdb=" N MET A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 346 through 364 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 4.033A pdb=" N CYS A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.952A pdb=" N MET A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 118 removed outlier: 3.700A pdb=" N GLY B 102 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.010A pdb=" N LYS B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.695A pdb=" N MET B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 346 through 364 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 removed outlier: 4.032A pdb=" N CYS B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 510 through 526 removed outlier: 3.952A pdb=" N MET B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 118 removed outlier: 3.699A pdb=" N GLY C 102 " --> pdb=" O MET C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.011A pdb=" N LYS C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.696A pdb=" N MET C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 346 through 364 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 4.033A pdb=" N CYS C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 453 No H-bonds generated for 'chain 'C' and resid 451 through 453' Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 510 through 526 removed outlier: 3.951A pdb=" N MET C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR A 311 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER A 261 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 207 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.408A pdb=" N VAL A 134 " --> pdb=" O MET A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN A 232 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 143 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR B 311 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 261 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 207 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.406A pdb=" N VAL B 134 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN B 232 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 143 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 311 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER C 261 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 207 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 135 removed outlier: 4.408A pdb=" N VAL C 134 " --> pdb=" O MET C 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN C 232 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 143 " --> pdb=" O ASN C 232 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3708 1.34 - 1.46: 2811 1.46 - 1.58: 5271 1.58 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 11904 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 11899 not shown) Histogram of bond angle deviations from ideal: 97.44 - 104.76: 204 104.76 - 112.08: 5980 112.08 - 119.41: 3851 119.41 - 126.73: 5929 126.73 - 134.05: 140 Bond angle restraints: 16104 Sorted by residual: angle pdb=" C TYR B 230 " pdb=" N PHE B 231 " pdb=" CA PHE B 231 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C TYR A 230 " pdb=" N PHE A 231 " pdb=" CA PHE A 231 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C TYR C 230 " pdb=" N PHE C 231 " pdb=" CA PHE C 231 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" CB ARG C 391 " pdb=" CG ARG C 391 " pdb=" CD ARG C 391 " ideal model delta sigma weight residual 111.30 101.30 10.00 2.30e+00 1.89e-01 1.89e+01 angle pdb=" CB ARG B 391 " pdb=" CG ARG B 391 " pdb=" CD ARG B 391 " ideal model delta sigma weight residual 111.30 101.31 9.99 2.30e+00 1.89e-01 1.89e+01 ... (remaining 16099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6858 17.81 - 35.62: 604 35.62 - 53.43: 114 53.43 - 71.24: 26 71.24 - 89.06: 30 Dihedral angle restraints: 7632 sinusoidal: 3522 harmonic: 4110 Sorted by residual: dihedral pdb=" CB CYS B 210 " pdb=" SG CYS B 210 " pdb=" SG CYS B 217 " pdb=" CB CYS B 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.73 -65.27 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " pdb=" SG CYS A 217 " pdb=" CB CYS A 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.74 -65.26 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS C 210 " pdb=" SG CYS C 210 " pdb=" SG CYS C 217 " pdb=" CB CYS C 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.76 -65.24 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 1847 0.196 - 0.393: 7 0.393 - 0.589: 6 0.589 - 0.785: 1 0.785 - 0.982: 2 Chirality restraints: 1863 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 401 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 169 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.20 0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 221 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 1860 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 221 " -0.003 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" CG ASN C 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 221 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN C 221 " 0.231 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.115 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" CG ASN C 331 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 221 " -0.025 2.00e-02 2.50e+03 1.12e-01 1.56e+02 pdb=" CG ASN A 221 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 221 " 0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN A 221 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.137 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 105 2.59 - 3.17: 9651 3.17 - 3.75: 17018 3.75 - 4.32: 24321 4.32 - 4.90: 40463 Nonbonded interactions: 91558 Sorted by model distance: nonbonded pdb=" OD1 ASN C 169 " pdb=" C1 NAG N 1 " model vdw 2.017 2.776 nonbonded pdb=" OD1 ASN C 393 " pdb=" C1 NAG L 1 " model vdw 2.131 2.776 nonbonded pdb=" OD1 ASP A 166 " pdb=" NH1 ARG A 391 " model vdw 2.236 2.520 nonbonded pdb=" OD1 ASP B 166 " pdb=" NH1 ARG B 391 " model vdw 2.236 2.520 nonbonded pdb=" ND2 ASN A 221 " pdb=" N2 NAG G 1 " model vdw 2.236 2.560 ... (remaining 91553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 91 through 577 or resid 701 through 702)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.400 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.490 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 0.080 11904 Z= 0.433 Angle : 0.821 10.396 16104 Z= 0.430 Chirality : 0.066 0.982 1863 Planarity : 0.004 0.046 2037 Dihedral : 14.939 89.055 4920 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.48 % Allowed : 0.71 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1389 helix: -0.16 (0.21), residues: 570 sheet: 0.74 (0.31), residues: 231 loop : -1.39 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 564 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.002 PHE C 554 TYR 0.017 0.002 TYR C 448 ARG 0.019 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 561 LEU cc_start: 0.8126 (mt) cc_final: 0.7867 (mt) REVERT: B 247 MET cc_start: 0.9039 (mmm) cc_final: 0.8796 (tpt) REVERT: B 561 LEU cc_start: 0.8082 (mt) cc_final: 0.7394 (mp) REVERT: C 561 LEU cc_start: 0.8134 (mt) cc_final: 0.7767 (mt) outliers start: 6 outliers final: 0 residues processed: 92 average time/residue: 1.3332 time to fit residues: 133.2590 Evaluate side-chains 60 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11904 Z= 0.182 Angle : 0.627 8.133 16104 Z= 0.317 Chirality : 0.046 0.451 1863 Planarity : 0.004 0.040 2037 Dihedral : 7.640 59.435 2154 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.95 % Allowed : 6.10 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1389 helix: 0.73 (0.22), residues: 552 sheet: 0.80 (0.31), residues: 237 loop : -1.17 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 564 HIS 0.002 0.001 HIS A 292 PHE 0.011 0.001 PHE A 222 TYR 0.008 0.001 TYR C 156 ARG 0.007 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7423 (tpp) cc_final: 0.6948 (tpp) REVERT: A 554 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7644 (t80) REVERT: B 475 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8465 (mtm) REVERT: B 554 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7437 (t80) REVERT: B 561 LEU cc_start: 0.7772 (mt) cc_final: 0.7377 (mt) REVERT: C 554 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6338 (t80) REVERT: C 561 LEU cc_start: 0.8048 (mt) cc_final: 0.7816 (mt) outliers start: 12 outliers final: 1 residues processed: 72 average time/residue: 1.2446 time to fit residues: 98.5350 Evaluate side-chains 61 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11904 Z= 0.219 Angle : 0.595 7.953 16104 Z= 0.301 Chirality : 0.046 0.445 1863 Planarity : 0.003 0.041 2037 Dihedral : 7.030 58.988 2154 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.79 % Allowed : 8.87 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1389 helix: 0.99 (0.23), residues: 552 sheet: 0.95 (0.32), residues: 237 loop : -1.10 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 564 HIS 0.003 0.001 HIS A 283 PHE 0.008 0.001 PHE C 226 TYR 0.013 0.001 TYR B 448 ARG 0.003 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7423 (tpp) cc_final: 0.6849 (tpp) REVERT: A 554 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 475 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8597 (mtm) REVERT: B 554 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7257 (t80) REVERT: B 561 LEU cc_start: 0.7713 (mt) cc_final: 0.7327 (mt) REVERT: C 98 MET cc_start: 0.7276 (tpt) cc_final: 0.6831 (tpp) REVERT: C 333 THR cc_start: 0.9087 (p) cc_final: 0.8855 (t) REVERT: C 554 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6515 (t80) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 1.1423 time to fit residues: 85.9338 Evaluate side-chains 65 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11904 Z= 0.208 Angle : 0.580 7.851 16104 Z= 0.293 Chirality : 0.045 0.449 1863 Planarity : 0.003 0.040 2037 Dihedral : 6.694 57.783 2154 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.79 % Allowed : 10.85 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1389 helix: 1.15 (0.23), residues: 537 sheet: 0.88 (0.32), residues: 240 loop : -0.94 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS C 283 PHE 0.009 0.001 PHE C 226 TYR 0.012 0.001 TYR B 448 ARG 0.002 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7462 (tpp) cc_final: 0.7007 (tpp) REVERT: A 554 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7356 (t80) REVERT: B 475 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8389 (mtm) REVERT: B 554 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7149 (t80) REVERT: B 561 LEU cc_start: 0.7692 (mt) cc_final: 0.7197 (mt) REVERT: C 98 MET cc_start: 0.7425 (tpt) cc_final: 0.6991 (tpp) REVERT: C 333 THR cc_start: 0.9086 (p) cc_final: 0.8868 (t) REVERT: C 554 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.6502 (t80) outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 1.0945 time to fit residues: 79.1818 Evaluate side-chains 66 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11904 Z= 0.334 Angle : 0.631 8.400 16104 Z= 0.315 Chirality : 0.048 0.483 1863 Planarity : 0.004 0.043 2037 Dihedral : 6.687 58.318 2154 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.50 % Allowed : 11.16 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1389 helix: 1.16 (0.23), residues: 540 sheet: 0.65 (0.32), residues: 246 loop : -0.96 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 564 HIS 0.004 0.001 HIS C 283 PHE 0.012 0.002 PHE C 226 TYR 0.018 0.001 TYR B 448 ARG 0.003 0.000 ARG C 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7296 (t80) REVERT: B 554 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7149 (t80) REVERT: B 561 LEU cc_start: 0.7833 (mt) cc_final: 0.7631 (mt) REVERT: C 98 MET cc_start: 0.7686 (tpt) cc_final: 0.7127 (tpp) REVERT: C 554 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6496 (t80) outliers start: 19 outliers final: 6 residues processed: 71 average time/residue: 1.0833 time to fit residues: 85.8289 Evaluate side-chains 67 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN C 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11904 Z= 0.184 Angle : 0.559 7.816 16104 Z= 0.284 Chirality : 0.045 0.446 1863 Planarity : 0.003 0.040 2037 Dihedral : 6.334 56.440 2154 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.74 % Allowed : 11.40 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1389 helix: 1.27 (0.23), residues: 540 sheet: 0.98 (0.32), residues: 237 loop : -0.86 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.002 0.001 HIS B 283 PHE 0.009 0.001 PHE C 226 TYR 0.011 0.001 TYR B 448 ARG 0.001 0.000 ARG B 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7506 (tpp) cc_final: 0.7127 (tpp) REVERT: A 554 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: B 98 MET cc_start: 0.7216 (tpp) cc_final: 0.6931 (tpp) REVERT: B 554 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: C 98 MET cc_start: 0.7519 (tpt) cc_final: 0.7079 (tpp) outliers start: 22 outliers final: 9 residues processed: 79 average time/residue: 0.8941 time to fit residues: 79.9461 Evaluate side-chains 70 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN C 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11904 Z= 0.166 Angle : 0.546 7.621 16104 Z= 0.277 Chirality : 0.045 0.430 1863 Planarity : 0.003 0.039 2037 Dihedral : 6.114 55.855 2154 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.74 % Allowed : 12.11 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1389 helix: 1.28 (0.23), residues: 543 sheet: 1.04 (0.32), residues: 237 loop : -0.77 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.002 0.001 HIS C 201 PHE 0.008 0.001 PHE C 226 TYR 0.010 0.001 TYR B 448 ARG 0.001 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7374 (tpp) cc_final: 0.6958 (tpp) REVERT: B 98 MET cc_start: 0.7191 (tpp) cc_final: 0.6834 (tpp) REVERT: B 475 MET cc_start: 0.8683 (mtm) cc_final: 0.8298 (mtm) REVERT: C 98 MET cc_start: 0.7703 (tpt) cc_final: 0.7205 (tpp) outliers start: 22 outliers final: 11 residues processed: 80 average time/residue: 1.0357 time to fit residues: 92.5235 Evaluate side-chains 68 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN C 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11904 Z= 0.155 Angle : 0.540 7.710 16104 Z= 0.275 Chirality : 0.044 0.426 1863 Planarity : 0.003 0.038 2037 Dihedral : 5.901 55.440 2154 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.27 % Allowed : 13.06 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1389 helix: 1.37 (0.23), residues: 543 sheet: 1.04 (0.32), residues: 240 loop : -0.71 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.002 0.001 HIS A 292 PHE 0.008 0.001 PHE B 226 TYR 0.009 0.001 TYR B 448 ARG 0.001 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7371 (tpp) cc_final: 0.6921 (tpp) REVERT: B 98 MET cc_start: 0.7098 (tpp) cc_final: 0.6814 (tpp) REVERT: B 475 MET cc_start: 0.8738 (mtm) cc_final: 0.8327 (mtm) outliers start: 16 outliers final: 16 residues processed: 78 average time/residue: 1.0422 time to fit residues: 90.2512 Evaluate side-chains 74 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11904 Z= 0.182 Angle : 0.558 8.643 16104 Z= 0.281 Chirality : 0.045 0.433 1863 Planarity : 0.003 0.039 2037 Dihedral : 5.868 55.736 2154 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.50 % Allowed : 13.06 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1389 helix: 1.34 (0.23), residues: 543 sheet: 1.05 (0.32), residues: 240 loop : -0.71 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 PHE 0.009 0.001 PHE C 226 TYR 0.011 0.001 TYR B 448 ARG 0.001 0.000 ARG C 423 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7315 (tpp) cc_final: 0.6924 (tpp) REVERT: B 98 MET cc_start: 0.7108 (tpp) cc_final: 0.6826 (tpp) REVERT: B 475 MET cc_start: 0.8756 (mtm) cc_final: 0.8496 (mtm) outliers start: 19 outliers final: 15 residues processed: 79 average time/residue: 0.9689 time to fit residues: 85.7483 Evaluate side-chains 74 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 86 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11904 Z= 0.225 Angle : 0.583 10.386 16104 Z= 0.293 Chirality : 0.046 0.447 1863 Planarity : 0.003 0.041 2037 Dihedral : 5.952 56.423 2154 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.27 % Allowed : 13.78 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1389 helix: 1.30 (0.23), residues: 543 sheet: 1.12 (0.32), residues: 237 loop : -0.71 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 564 HIS 0.003 0.001 HIS C 283 PHE 0.009 0.001 PHE C 226 TYR 0.013 0.001 TYR B 448 ARG 0.002 0.000 ARG B 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7451 (tpp) cc_final: 0.7014 (tpp) REVERT: B 475 MET cc_start: 0.8773 (mtm) cc_final: 0.8378 (mtm) REVERT: C 98 MET cc_start: 0.7586 (tpt) cc_final: 0.7367 (tpp) REVERT: C 363 CYS cc_start: 0.6478 (OUTLIER) cc_final: 0.6169 (p) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 1.0173 time to fit residues: 88.6112 Evaluate side-chains 72 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.075531 restraints weight = 17859.552| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.76 r_work: 0.2851 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11904 Z= 0.177 Angle : 0.562 8.451 16104 Z= 0.283 Chirality : 0.045 0.435 1863 Planarity : 0.003 0.040 2037 Dihedral : 5.852 56.024 2154 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.35 % Allowed : 14.01 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1389 helix: 1.32 (0.23), residues: 543 sheet: 1.05 (0.32), residues: 240 loop : -0.69 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 564 HIS 0.002 0.001 HIS A 283 PHE 0.008 0.001 PHE C 226 TYR 0.011 0.001 TYR B 448 ARG 0.001 0.000 ARG A 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.56 seconds wall clock time: 58 minutes 35.51 seconds (3515.51 seconds total)