Starting phenix.real_space_refine (version: dev) on Mon Feb 20 19:02:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/02_2023/7nxd_12637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/02_2023/7nxd_12637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/02_2023/7nxd_12637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/02_2023/7nxd_12637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/02_2023/7nxd_12637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/02_2023/7nxd_12637.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 6": "NH1" <-> "NH2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12805 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 6953 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 58, 'TRANS': 846} Chain breaks: 2 Chain: "B" Number of atoms: 5314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5314 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 25, 'TRANS': 664} Chain breaks: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 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 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 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 19 Unusual residues: {' CA': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" N ALA A 784 " occ=0.66 ... (3 atoms not shown) pdb=" CB ALA A 784 " occ=0.66 residue: pdb=" N TYR A 789 " occ=0.66 ... (10 atoms not shown) pdb=" OH TYR A 789 " occ=0.66 residue: pdb=" N GLU A 790 " occ=0.66 ... (7 atoms not shown) pdb=" OE2 GLU A 790 " occ=0.66 residue: pdb=" N LEU A 882 " occ=0.66 ... (6 atoms not shown) pdb=" CD2 LEU A 882 " occ=0.66 residue: pdb=" N TRP A 900 " occ=0.66 ... (12 atoms not shown) pdb=" CH2 TRP A 900 " occ=0.66 residue: pdb=" N PRO A 926 " occ=0.66 ... (5 atoms not shown) pdb=" CD PRO A 926 " occ=0.66 residue: pdb=" N TYR A 927 " occ=0.66 ... (10 atoms not shown) pdb=" OH TYR A 927 " occ=0.66 residue: pdb=" N GLY B 618 " occ=0.75 ... (2 atoms not shown) pdb=" O GLY B 618 " occ=0.75 residue: pdb=" N CYS B 620 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 620 " occ=0.75 residue: pdb=" N LYS B 624 " occ=0.75 ... (7 atoms not shown) pdb=" NZ LYS B 624 " occ=0.75 residue: pdb=" N GLU B 625 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 625 " occ=0.75 residue: pdb=" N CYS B 626 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 626 " occ=0.75 ... (remaining 16 not shown) Time building chain proxies: 7.99, per 1000 atoms: 0.62 Number of scatterers: 12805 At special positions: 0 Unit cell: (104.55, 136, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 94 16.00 Mg 1 11.99 O 2613 8.00 N 2142 7.00 C 7948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 690 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 916 " distance=2.03 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 880 " distance=2.03 Simple disulfide: pdb=" SG CYS A 870 " - pdb=" SG CYS A 875 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.04 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=1.83 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.30 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=1.92 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 457 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 513 " distance=2.02 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 548 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 595 " distance=2.03 Simple disulfide: pdb=" SG CYS B 579 " - pdb=" SG CYS B 593 " distance=2.02 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 610 " distance=2.04 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 616 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS B 629 " - pdb=" SG CYS B 641 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 703 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 6 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " BETA1-2 " MAN G 4 " - " NAG G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A1106 " - " ASN A 483 " " NAG C 1 " - " ASN A 43 " " NAG D 1 " - " ASN A 141 " " NAG E 1 " - " ASN A 256 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN A 568 " " NAG I 1 " - " ASN A 489 " " NAG J 1 " - " ASN B 192 " " NAG K 1 " - " ASN B 249 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 386 " " NAG N 1 " - " ASN B 397 " " NAG O 1 " - " ASN B 461 " " NAG P 1 " - " ASN B 30 " Time building additional restraints: 6.27 Conformation dependent library (CDL) restraints added in 1.9 seconds 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 29 sheets defined 12.9% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 509 through 512 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.731A pdb=" N ARG A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.702A pdb=" N CYS B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 19 " --> pdb=" O CYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 42 Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.590A pdb=" N GLY B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 157 removed outlier: 3.509A pdb=" N ASN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.813A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 removed outlier: 4.040A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.705A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.834A pdb=" N ASN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.503A pdb=" N GLY B 549 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.728A pdb=" N SER A 437 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 418 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.025A pdb=" N TYR A 26 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A 34 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 55 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 4.093A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 4.061A pdb=" N THR A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 144 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.580A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 217 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.106A pdb=" N SER A 234 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 274 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN A 266 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER A 272 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 288 through 292 removed outlier: 3.578A pdb=" N ALA A 288 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 326 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 340 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.637A pdb=" N GLN A 319 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.780A pdb=" N VAL A 369 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 384 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 402 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 386 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 519 through 521 removed outlier: 3.510A pdb=" N LEU A 488 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 544 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 486 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A 485 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 459 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 489 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 491 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=AB4, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=AB5, first strand: chain 'A' and resid 614 through 621 removed outlier: 3.555A pdb=" N GLU A 621 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 634 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 664 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR A 709 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 662 " --> pdb=" O THR A 709 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 677 through 680 removed outlier: 3.743A pdb=" N LEU A 687 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 688 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA A 650 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 725 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 723 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 751 through 757 removed outlier: 6.304A pdb=" N GLN A 894 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 823 " --> pdb=" O GLN A 894 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS A 896 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 828 through 830 removed outlier: 3.655A pdb=" N LEU A 804 " --> pdb=" O CYS A 880 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN A 801 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 923 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 866 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLN A 915 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 868 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLU A 917 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 828 through 830 removed outlier: 3.655A pdb=" N LEU A 804 " --> pdb=" O CYS A 880 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN A 801 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 923 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.060A pdb=" N LEU B 99 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 423 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.654A pdb=" N GLN B 109 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.654A pdb=" N GLN B 109 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 199 through 201 removed outlier: 7.062A pdb=" N ILE B 123 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY B 163 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 125 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B 165 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR B 127 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE B 167 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N MET B 129 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B 124 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 255 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 126 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N SER B 257 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 128 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 258 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 317 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AC7, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AC8, first strand: chain 'B' and resid 509 through 512 removed outlier: 3.514A pdb=" N VAL B 517 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 512 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AD1, first strand: chain 'B' and resid 592 through 594 removed outlier: 3.898A pdb=" N GLU B 594 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 671 through 674 removed outlier: 3.590A pdb=" N PHE B 683 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 673 " --> pdb=" O PHE B 681 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 879 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: 4.64 Time building geometry restraints manager: 6.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2648 1.33 - 1.45: 3073 1.45 - 1.58: 7218 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 13051 Sorted by residual: bond pdb=" N CYS B 415 " pdb=" CA CYS B 415 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.10e-03 1.21e+04 1.51e+01 bond pdb=" N GLU A 126 " pdb=" CA GLU A 126 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" N LYS B 87 " pdb=" CA LYS B 87 " ideal model delta sigma weight residual 1.456 1.488 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.17e-02 7.31e+03 1.30e+01 bond pdb=" N VAL A 756 " pdb=" CA VAL A 756 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.29e+01 ... (remaining 13046 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.74: 430 106.74 - 113.64: 7216 113.64 - 120.54: 5568 120.54 - 127.43: 4400 127.43 - 134.33: 64 Bond angle restraints: 17678 Sorted by residual: angle pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 109.64 117.02 -7.38 5.38e-01 3.45e+00 1.88e+02 angle pdb=" C2 NAG I 1 " pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 109.64 116.27 -6.63 5.38e-01 3.45e+00 1.52e+02 angle pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 109.64 114.71 -5.07 5.38e-01 3.45e+00 8.87e+01 angle pdb=" C2 NAG P 2 " pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 109.64 114.24 -4.60 5.38e-01 3.45e+00 7.31e+01 angle pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " ideal model delta sigma weight residual 110.19 117.87 -7.68 9.25e-01 1.17e+00 6.89e+01 ... (remaining 17673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7521 17.99 - 35.99: 319 35.99 - 53.98: 55 53.98 - 71.97: 15 71.97 - 89.97: 7 Dihedral angle restraints: 7917 sinusoidal: 3373 harmonic: 4544 Sorted by residual: dihedral pdb=" CB CYS B 457 " pdb=" SG CYS B 457 " pdb=" SG CYS B 469 " pdb=" CB CYS B 469 " ideal model delta sinusoidal sigma weight residual -86.00 -175.97 89.97 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 481 " pdb=" CB CYS A 481 " ideal model delta sinusoidal sigma weight residual -86.00 -170.83 84.83 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 7914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 1824 0.169 - 0.337: 206 0.337 - 0.506: 6 0.506 - 0.674: 0 0.674 - 0.843: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.78e+03 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.48e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.66e+02 ... (remaining 2034 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " -0.360 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG O 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " 0.551 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.351 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG G 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.099 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG E 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.150 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 9052 3.06 - 3.67: 18096 3.67 - 4.29: 26307 4.29 - 4.90: 43308 Nonbonded interactions: 96864 Sorted by model distance: nonbonded pdb=" O SER B 134 " pdb="CA CA B1002 " model vdw 1.831 2.510 nonbonded pdb=" OD1 ASP A 243 " pdb="CA CA A1101 " model vdw 1.885 2.510 nonbonded pdb=" OG SER A 241 " pdb="CA CA A1101 " model vdw 1.904 2.510 nonbonded pdb=" OD1 ASN A 428 " pdb="CA CA A1104 " model vdw 1.914 2.510 nonbonded pdb=" OD2 ASP B 226 " pdb="CA CA B1003 " model vdw 2.011 2.510 ... (remaining 96859 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 'C' selection = chain 'E' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 94 5.16 5 C 7948 2.51 5 N 2142 2.21 5 O 2613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 7.580 Check model and map are aligned: 0.180 Process input model: 38.270 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4448 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 : 0.013 0.050 13051 Z= 0.871 Angle : 1.484 8.678 17678 Z= 1.149 Chirality : 0.107 0.843 2037 Planarity : 0.029 0.310 2295 Dihedral : 9.177 74.975 4906 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 64.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1583 helix: 1.10 (0.49), residues: 132 sheet: -0.17 (0.24), residues: 460 loop : -1.21 (0.18), residues: 991 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 193 average time/residue: 0.3139 time to fit residues: 82.2720 Evaluate side-chains 98 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.208 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1080 time to fit residues: 2.9215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 165 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS A 587 HIS A 787 HIS A 801 GLN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 74 ASN B 77 ASN B 93 GLN B 309 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 623 HIS B 628 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 HIS ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4827 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 13051 Z= 0.366 Angle : 0.853 10.314 17678 Z= 0.468 Chirality : 0.058 1.001 2037 Planarity : 0.006 0.082 2295 Dihedral : 5.225 21.841 1992 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1583 helix: 0.28 (0.39), residues: 149 sheet: 0.02 (0.23), residues: 486 loop : -1.00 (0.18), residues: 948 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.3011 time to fit residues: 46.4396 Evaluate side-chains 75 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 0.0670 chunk 143 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS A 816 GLN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN B 349 GLN ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4803 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 13051 Z= 0.236 Angle : 0.656 6.365 17678 Z= 0.359 Chirality : 0.051 0.781 2037 Planarity : 0.004 0.059 2295 Dihedral : 4.825 19.291 1992 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1583 helix: 0.46 (0.40), residues: 153 sheet: 0.22 (0.23), residues: 488 loop : -0.80 (0.19), residues: 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2987 time to fit residues: 39.2868 Evaluate side-chains 64 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 633 ASN ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4886 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 13051 Z= 0.223 Angle : 0.625 11.594 17678 Z= 0.339 Chirality : 0.050 0.807 2037 Planarity : 0.004 0.058 2295 Dihedral : 4.851 21.542 1992 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1583 helix: 0.74 (0.42), residues: 152 sheet: 0.15 (0.22), residues: 510 loop : -0.75 (0.20), residues: 921 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3094 time to fit residues: 37.2744 Evaluate side-chains 61 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5222 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 13051 Z= 0.439 Angle : 0.915 12.539 17678 Z= 0.491 Chirality : 0.053 0.669 2037 Planarity : 0.006 0.057 2295 Dihedral : 5.975 33.451 1992 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 39.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1583 helix: -0.66 (0.38), residues: 149 sheet: -0.34 (0.22), residues: 507 loop : -1.12 (0.19), residues: 927 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.2837 time to fit residues: 30.3770 Evaluate side-chains 53 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1146 time to fit residues: 2.1529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13051 Z= 0.252 Angle : 0.687 11.155 17678 Z= 0.369 Chirality : 0.051 0.936 2037 Planarity : 0.004 0.060 2295 Dihedral : 5.547 26.506 1992 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 26.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1583 helix: -0.19 (0.40), residues: 150 sheet: -0.24 (0.22), residues: 516 loop : -1.01 (0.20), residues: 917 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2655 time to fit residues: 26.7263 Evaluate side-chains 51 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 0.0050 chunk 93 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5146 moved from start: 0.7506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13051 Z= 0.264 Angle : 0.694 11.682 17678 Z= 0.371 Chirality : 0.051 0.806 2037 Planarity : 0.004 0.057 2295 Dihedral : 5.525 26.672 1992 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 28.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1583 helix: -0.23 (0.40), residues: 151 sheet: -0.25 (0.22), residues: 514 loop : -0.96 (0.20), residues: 918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2574 time to fit residues: 23.8254 Evaluate side-chains 46 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13051 Z= 0.200 Angle : 0.634 10.485 17678 Z= 0.339 Chirality : 0.050 0.766 2037 Planarity : 0.004 0.057 2295 Dihedral : 5.352 26.958 1992 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1583 helix: -0.10 (0.41), residues: 155 sheet: -0.25 (0.22), residues: 519 loop : -0.90 (0.20), residues: 909 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2449 time to fit residues: 22.2133 Evaluate side-chains 47 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 8.9990 chunk 142 optimal weight: 0.0170 chunk 146 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 129 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 151 optimal weight: 4.9990 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 GLN B 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5046 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13051 Z= 0.180 Angle : 0.613 13.112 17678 Z= 0.323 Chirality : 0.049 0.731 2037 Planarity : 0.004 0.056 2295 Dihedral : 5.130 28.150 1992 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1583 helix: 0.05 (0.41), residues: 155 sheet: -0.08 (0.22), residues: 511 loop : -0.88 (0.20), residues: 917 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2296 time to fit residues: 22.7255 Evaluate side-chains 52 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 564 ASN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5163 moved from start: 0.8152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13051 Z= 0.241 Angle : 0.658 12.055 17678 Z= 0.351 Chirality : 0.049 0.725 2037 Planarity : 0.004 0.055 2295 Dihedral : 5.334 28.572 1992 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1583 helix: -0.18 (0.40), residues: 155 sheet: -0.10 (0.22), residues: 487 loop : -0.89 (0.20), residues: 941 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.2304 time to fit residues: 22.1404 Evaluate side-chains 51 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN A 787 HIS ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 98 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.068230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.049621 restraints weight = 164309.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.049920 restraints weight = 152043.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.049921 restraints weight = 142432.445| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 199 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.9498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 13051 Z= 0.280 Angle : 0.735 13.015 17678 Z= 0.394 Chirality : 0.051 0.736 2037 Planarity : 0.005 0.059 2295 Dihedral : 5.953 35.388 1992 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 35.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1583 helix: -0.95 (0.36), residues: 168 sheet: -0.49 (0.23), residues: 490 loop : -1.13 (0.20), residues: 925 =============================================================================== Job complete usr+sys time: 2273.63 seconds wall clock time: 42 minutes 57.07 seconds (2577.07 seconds total)