Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 02:30:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/07_2023/7uaf_26423_updated.pdb" } resolution = 2.4 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= 0.002 sd= 0.036 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 S 84 5.16 5 C 11246 2.51 5 N 2979 2.21 5 O 3543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B ARG 546": "NH1" <-> "NH2" Residue "B ARG 549": "NH1" <-> "NH2" Residue "B PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C GLU 514": "OE1" <-> "OE2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C ARG 549": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 502": "OE1" <-> "OE2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D GLU 514": "OE1" <-> "OE2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 546": "NH1" <-> "NH2" Residue "D ARG 549": "NH1" <-> "NH2" Residue "D ARG 578": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 17864 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4319 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4313 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4295 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 512} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4257 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 509} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 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 chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" 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: "Q" 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: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.96, per 1000 atoms: 0.50 Number of scatterers: 17864 At special positions: 0 Unit cell: (110.24, 168.54, 135.68, 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) Zn 4 29.99 Ca 8 19.99 S 84 16.00 O 3543 8.00 N 2979 7.00 C 11246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 147 " distance=1.99 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS A 308 " distance=2.05 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 431 " distance=2.06 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS B 559 " distance=2.04 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.06 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 259 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 431 " distance=2.05 Simple disulfide: pdb=" SG CYS C 557 " - pdb=" SG CYS C 559 " distance=2.05 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 259 " distance=2.04 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 147 " distance=2.01 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 277 " distance=2.04 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 431 " distance=2.06 Simple disulfide: pdb=" SG CYS D 557 " - pdb=" SG CYS D 559 " distance=2.05 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " BETA1-6 " NAG H 1 " - " FUC H 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " " NAG R 1 " - " FUC R 4 " NAG-ASN " NAG A 705 " - " ASN A 440 " " NAG B 705 " - " ASN B 440 " " NAG C 705 " - " ASN C 440 " " NAG D 705 " - " ASN D 440 " " NAG E 1 " - " ASN B 140 " " NAG F 1 " - " ASN B 258 " " NAG G 1 " - " ASN B 222 " " NAG H 1 " - " ASN B 414 " " NAG I 1 " - " ASN A 258 " " NAG J 1 " - " ASN A 222 " " NAG K 1 " - " ASN A 414 " " NAG L 1 " - " ASN A 140 " " NAG M 1 " - " ASN C 140 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 414 " " NAG P 1 " - " ASN D 140 " " NAG Q 1 " - " ASN D 222 " " NAG R 1 " - " ASN D 414 " Time building additional restraints: 8.40 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 155 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 159 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 165 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 155 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 159 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 165 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 155 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 159 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 165 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 155 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 159 " 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 31 sheets defined 17.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 89 through 105 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 441 through 447 removed outlier: 3.505A pdb=" N GLU B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 547 through 550 No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 597 through 599 No H-bonds generated for 'chain 'B' and resid 597 through 599' Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 89 through 105 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' Processing helix chain 'A' and resid 547 through 550 No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 573 through 576 No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 89 through 105 Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 188 through 191 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 441 through 447 removed outlier: 4.146A pdb=" N GLU C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 547 through 550 No H-bonds generated for 'chain 'C' and resid 547 through 550' Processing helix chain 'C' and resid 573 through 576 No H-bonds generated for 'chain 'C' and resid 573 through 576' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 89 through 105 Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 441 through 447 removed outlier: 4.031A pdb=" N GLU D 446 " --> pdb=" O SER D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 536 through 538 No H-bonds generated for 'chain 'D' and resid 536 through 538' Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 597 through 599 No H-bonds generated for 'chain 'D' and resid 597 through 599' Processing sheet with id= A, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.036A pdb=" N ILE B 79 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 120 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN B 139 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLN B 123 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 141 " --> pdb=" O GLN B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 176 through 178 Processing sheet with id= C, first strand: chain 'B' and resid 290 through 292 Processing sheet with id= D, first strand: chain 'B' and resid 327 through 331 removed outlier: 6.064A pdb=" N VAL B 362 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS B 376 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG B 364 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 374 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 343 through 345 Processing sheet with id= F, first strand: chain 'B' and resid 434 through 438 Processing sheet with id= G, first strand: chain 'B' and resid 466 through 472 removed outlier: 3.951A pdb=" N GLY B 466 " --> pdb=" O CYS B 489 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 571 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 484 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY B 569 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE B 486 " --> pdb=" O TRP B 567 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N TRP B 567 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 488 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N LEU B 565 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 552 through 554 Processing sheet with id= I, first strand: chain 'A' and resid 110 through 112 removed outlier: 5.958A pdb=" N ILE A 79 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 120 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN A 139 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN A 123 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 141 " --> pdb=" O GLN A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 176 through 178 Processing sheet with id= K, first strand: chain 'A' and resid 290 through 292 Processing sheet with id= L, first strand: chain 'A' and resid 327 through 331 removed outlier: 6.171A pdb=" N VAL A 362 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS A 376 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG A 364 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 374 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 343 through 345 Processing sheet with id= N, first strand: chain 'A' and resid 434 through 438 Processing sheet with id= O, first strand: chain 'A' and resid 466 through 472 removed outlier: 3.983A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.082A pdb=" N ILE C 79 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 120 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN C 139 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN C 123 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 141 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 176 through 178 Processing sheet with id= R, first strand: chain 'C' and resid 290 through 292 Processing sheet with id= S, first strand: chain 'C' and resid 327 through 331 removed outlier: 6.246A pdb=" N VAL C 362 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS C 376 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG C 364 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU C 374 " --> pdb=" O ARG C 364 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 343 through 345 Processing sheet with id= U, first strand: chain 'C' and resid 434 through 438 Processing sheet with id= V, first strand: chain 'C' and resid 466 through 472 removed outlier: 3.828A pdb=" N GLY C 466 " --> pdb=" O CYS C 489 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 571 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 484 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLY C 569 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N PHE C 486 " --> pdb=" O TRP C 567 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TRP C 567 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL C 488 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU C 565 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= X, first strand: chain 'D' and resid 110 through 112 removed outlier: 6.008A pdb=" N ILE D 79 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 120 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN D 139 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLN D 123 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 141 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 176 through 178 Processing sheet with id= Z, first strand: chain 'D' and resid 290 through 292 Processing sheet with id= AA, first strand: chain 'D' and resid 327 through 331 removed outlier: 6.184A pdb=" N VAL D 362 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS D 376 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU D 374 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 343 through 345 Processing sheet with id= AC, first strand: chain 'D' and resid 434 through 438 Processing sheet with id= AD, first strand: chain 'D' and resid 466 through 472 removed outlier: 3.863A pdb=" N GLY D 466 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE D 571 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU D 484 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY D 569 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE D 486 " --> pdb=" O TRP D 567 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TRP D 567 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL D 488 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LEU D 565 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 551 through 554 442 hydrogen bonds defined for protein. 1149 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: 5.33 Time building geometry restraints manager: 8.65 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: 4866 1.33 - 1.45: 3929 1.45 - 1.58: 9386 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 18301 Sorted by residual: bond pdb=" C13 M6X D 701 " pdb=" N2 M6X D 701 " ideal model delta sigma weight residual 1.451 1.311 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C13 M6X A 701 " pdb=" N2 M6X A 701 " ideal model delta sigma weight residual 1.451 1.311 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C13 M6X B 701 " pdb=" N2 M6X B 701 " ideal model delta sigma weight residual 1.451 1.311 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C13 M6X C 701 " pdb=" N2 M6X C 701 " ideal model delta sigma weight residual 1.451 1.311 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C VAL A 300 " pdb=" N ASP A 301 " ideal model delta sigma weight residual 1.328 1.246 0.082 1.40e-02 5.10e+03 3.43e+01 ... (remaining 18296 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.71: 278 104.71 - 112.29: 7655 112.29 - 119.88: 8176 119.88 - 127.47: 8513 127.47 - 135.06: 213 Bond angle restraints: 24835 Sorted by residual: angle pdb=" N ARG D 284 " pdb=" CA ARG D 284 " pdb=" C ARG D 284 " ideal model delta sigma weight residual 112.23 104.24 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" C THR C 433 " pdb=" N GLY C 434 " pdb=" CA GLY C 434 " ideal model delta sigma weight residual 121.65 125.87 -4.22 6.80e-01 2.16e+00 3.85e+01 angle pdb=" CA PHE D 590 " pdb=" CB PHE D 590 " pdb=" CG PHE D 590 " ideal model delta sigma weight residual 113.80 119.58 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" N ASP D 512 " pdb=" CA ASP D 512 " pdb=" C ASP D 512 " ideal model delta sigma weight residual 109.25 100.43 8.82 1.53e+00 4.27e-01 3.32e+01 angle pdb=" CA ASP C 301 " pdb=" CB ASP C 301 " pdb=" CG ASP C 301 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 ... (remaining 24830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 9813 21.11 - 42.22: 517 42.22 - 63.33: 82 63.33 - 84.44: 27 84.44 - 105.55: 9 Dihedral angle restraints: 10448 sinusoidal: 4256 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual 93.00 150.93 -57.93 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " pdb=" SG CYS D 559 " pdb=" CB CYS D 559 " ideal model delta sinusoidal sigma weight residual -86.00 -143.42 57.42 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C 557 " pdb=" SG CYS C 557 " pdb=" SG CYS C 559 " pdb=" CB CYS C 559 " ideal model delta sinusoidal sigma weight residual -86.00 -142.55 56.55 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 10445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1667 0.087 - 0.174: 849 0.174 - 0.262: 183 0.262 - 0.349: 42 0.349 - 0.436: 12 Chirality restraints: 2753 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 FUC H 4 " pdb=" O6 NAG H 1 " pdb=" C2 FUC H 4 " pdb=" O5 FUC H 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.07e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.88e+01 ... (remaining 2750 not shown) Planarity restraints: 3192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.319 2.00e-02 2.50e+03 2.75e-01 9.49e+02 pdb=" C7 NAG L 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.477 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 705 " -0.320 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG A 705 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 705 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 705 " 0.472 2.00e-02 2.50e+03 pdb=" O7 NAG A 705 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 705 " -0.318 2.00e-02 2.50e+03 2.70e-01 9.10e+02 pdb=" C7 NAG B 705 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B 705 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B 705 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG B 705 " -0.048 2.00e-02 2.50e+03 ... (remaining 3189 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 38 2.41 - 3.03: 10014 3.03 - 3.65: 25570 3.65 - 4.28: 44773 4.28 - 4.90: 70537 Nonbonded interactions: 150932 Sorted by model distance: nonbonded pdb=" O CYS D 128 " pdb=" O6 M6X D 701 " model vdw 1.783 2.440 nonbonded pdb=" OH TYR B 214 " pdb=" O3 M6X B 701 " model vdw 1.855 2.440 nonbonded pdb=" O CYS D 128 " pdb=" N2 M6X D 701 " model vdw 1.856 2.520 nonbonded pdb=" OD1 ASP B 285 " pdb="CA CA B 702 " model vdw 1.861 2.510 nonbonded pdb=" OH TYR A 214 " pdb=" O3 M6X A 701 " model vdw 1.999 2.440 ... (remaining 150927 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 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 295 or resid 299 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB )) or resid 334 thr \ ough 600 or resid 701 through 705)) selection = (chain 'B' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 295 or resid 299 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB )) or resid 334 thr \ ough 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 600 or resid 701 through 705)) selection = (chain 'C' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 475 or (resid 476 and (name N or nam \ e CA or name C or name O or name CB )) or resid 477 through 600 or resid 701 thr \ ough 705)) selection = (chain 'D' and (resid 66 through 295 or resid 299 through 475 or (resid 476 and \ (name N or name CA or name C or name O or name CB )) or resid 477 through 600 or \ resid 701 through 705)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'O' selection = chain 'R' } 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: 0.010 Normalize map: mean=0, sd=1: 0.640 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: 0.020 Extract box with map and model: 4.020 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 49.620 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.150 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.012 0.140 18301 Z= 0.795 Angle : 1.815 8.822 24835 Z= 1.215 Chirality : 0.105 0.436 2753 Planarity : 0.021 0.275 3174 Dihedral : 13.981 105.549 6409 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 10.53 % 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: -0.18 (0.17), residues: 2117 helix: -1.52 (0.27), residues: 259 sheet: 0.67 (0.21), residues: 515 loop : -0.08 (0.17), residues: 1343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 564 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 565 average time/residue: 1.3495 time to fit residues: 847.1761 Evaluate side-chains 466 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN B 145 GLN B 215 GLN B 307 GLN B 341 GLN B 413 GLN B 574 GLN A 66 ASN A 72 ASN A 145 GLN A 296 GLN A 447 ASN C 72 ASN C 189 HIS C 341 GLN C 513 GLN D 72 ASN D 136 HIS D 341 GLN D 513 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18301 Z= 0.210 Angle : 0.618 8.782 24835 Z= 0.331 Chirality : 0.046 0.178 2753 Planarity : 0.003 0.031 3174 Dihedral : 8.320 142.891 2380 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.29 (0.18), residues: 2117 helix: -0.22 (0.31), residues: 264 sheet: 0.49 (0.20), residues: 572 loop : 0.27 (0.17), residues: 1281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 474 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 17 residues processed: 495 average time/residue: 1.3882 time to fit residues: 761.3824 Evaluate side-chains 475 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 458 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 9 average time/residue: 0.4783 time to fit residues: 7.9445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 190 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 124 GLN B 145 GLN B 370 ASN B 558 ASN B 574 GLN A 399 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 291 HIS C 474 ASN D 341 GLN D 370 ASN D 558 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 18301 Z= 0.347 Angle : 0.623 7.354 24835 Z= 0.335 Chirality : 0.047 0.162 2753 Planarity : 0.004 0.048 3174 Dihedral : 7.830 122.691 2380 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.16 (0.18), residues: 2117 helix: 0.03 (0.32), residues: 264 sheet: 0.42 (0.21), residues: 583 loop : 0.08 (0.17), residues: 1270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 487 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 35 residues processed: 507 average time/residue: 1.3847 time to fit residues: 779.2998 Evaluate side-chains 505 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 470 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 17 residues processed: 22 average time/residue: 0.5741 time to fit residues: 18.9527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 86 ASN B 124 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN C 182 GLN C 189 HIS C 474 ASN C 574 GLN D 341 GLN D 345 GLN D 370 ASN D 558 ASN D 573 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18301 Z= 0.181 Angle : 0.528 6.826 24835 Z= 0.285 Chirality : 0.043 0.157 2753 Planarity : 0.003 0.035 3174 Dihedral : 7.379 118.265 2380 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.21 (0.18), residues: 2117 helix: 0.33 (0.33), residues: 264 sheet: 0.39 (0.21), residues: 585 loop : 0.07 (0.17), residues: 1268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 472 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 33 residues processed: 498 average time/residue: 1.3819 time to fit residues: 765.2857 Evaluate side-chains 490 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 457 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 18 residues processed: 19 average time/residue: 0.2676 time to fit residues: 10.4513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 0.0000 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 145 GLN B 188 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 66 ASN A 275 ASN A 455 GLN C 177 ASN C 182 GLN C 189 HIS C 215 GLN C 573 HIS C 574 GLN D 341 GLN D 345 GLN D 558 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 18301 Z= 0.345 Angle : 0.585 7.890 24835 Z= 0.314 Chirality : 0.046 0.150 2753 Planarity : 0.004 0.046 3174 Dihedral : 7.434 112.275 2380 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.07 (0.18), residues: 2117 helix: 0.20 (0.32), residues: 264 sheet: 0.44 (0.22), residues: 554 loop : -0.08 (0.17), residues: 1299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 461 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 38 residues processed: 501 average time/residue: 1.3927 time to fit residues: 775.3793 Evaluate side-chains 498 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 460 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 21 residues processed: 20 average time/residue: 0.6992 time to fit residues: 19.5617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 0.0030 chunk 50 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 145 GLN B 188 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 455 GLN A 474 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 215 GLN C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 18301 Z= 0.239 Angle : 0.535 6.473 24835 Z= 0.288 Chirality : 0.043 0.140 2753 Planarity : 0.003 0.040 3174 Dihedral : 7.191 108.304 2380 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.08 (0.18), residues: 2117 helix: 0.29 (0.32), residues: 264 sheet: 0.41 (0.22), residues: 558 loop : -0.08 (0.17), residues: 1295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 465 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 40 residues processed: 498 average time/residue: 1.4184 time to fit residues: 783.4079 Evaluate side-chains 502 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 462 time to evaluate : 1.989 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 24 residues processed: 19 average time/residue: 0.5436 time to fit residues: 16.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN B 443 GLN B 574 GLN C 182 GLN C 189 HIS C 215 GLN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 341 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 18301 Z= 0.204 Angle : 0.524 7.243 24835 Z= 0.281 Chirality : 0.043 0.140 2753 Planarity : 0.003 0.042 3174 Dihedral : 7.028 104.501 2380 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.18), residues: 2117 helix: 0.42 (0.33), residues: 264 sheet: 0.45 (0.22), residues: 555 loop : -0.04 (0.17), residues: 1298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 475 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 39 residues processed: 506 average time/residue: 1.3712 time to fit residues: 772.3550 Evaluate side-chains 499 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 460 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 23 residues processed: 18 average time/residue: 0.4662 time to fit residues: 13.9300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN B 443 GLN B 574 GLN C 177 ASN C 182 GLN C 189 HIS C 215 GLN C 574 GLN D 292 GLN D 341 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.077 18301 Z= 0.458 Angle : 0.637 7.804 24835 Z= 0.340 Chirality : 0.048 0.147 2753 Planarity : 0.004 0.048 3174 Dihedral : 7.430 106.888 2380 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.13 (0.18), residues: 2117 helix: 0.08 (0.31), residues: 264 sheet: 0.33 (0.22), residues: 556 loop : -0.24 (0.17), residues: 1297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 464 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 44 residues processed: 497 average time/residue: 1.4323 time to fit residues: 790.4718 Evaluate side-chains 505 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 461 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 27 residues processed: 20 average time/residue: 0.4902 time to fit residues: 16.4767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN B 443 GLN B 574 GLN C 177 ASN C 182 GLN C 189 HIS C 215 GLN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 341 GLN D 519 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 18301 Z= 0.201 Angle : 0.544 10.736 24835 Z= 0.290 Chirality : 0.043 0.141 2753 Planarity : 0.003 0.045 3174 Dihedral : 7.078 100.458 2380 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.00 (0.18), residues: 2117 helix: 0.35 (0.32), residues: 264 sheet: 0.34 (0.22), residues: 553 loop : -0.15 (0.17), residues: 1300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 465 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 35 residues processed: 493 average time/residue: 1.3972 time to fit residues: 767.6005 Evaluate side-chains 492 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 457 time to evaluate : 1.981 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 9 average time/residue: 0.5604 time to fit residues: 9.0677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 193 optimal weight: 0.1980 chunk 167 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 455 GLN C 177 ASN C 182 GLN C 189 HIS C 215 GLN C 574 GLN D 341 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18301 Z= 0.199 Angle : 0.541 10.741 24835 Z= 0.288 Chirality : 0.042 0.148 2753 Planarity : 0.004 0.053 3174 Dihedral : 6.973 97.539 2380 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2117 helix: 0.44 (0.33), residues: 264 sheet: 0.36 (0.22), residues: 566 loop : -0.12 (0.17), residues: 1287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 464 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 35 residues processed: 492 average time/residue: 1.4044 time to fit residues: 769.8408 Evaluate side-chains 496 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 461 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 29 residues processed: 8 average time/residue: 0.6302 time to fit residues: 8.6487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 154 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 316 GLN C 177 ASN C 182 GLN C 189 HIS C 215 GLN D 341 GLN D 558 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.136518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117808 restraints weight = 22402.897| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.72 r_work: 0.3449 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 18301 Z= 0.282 Angle : 0.573 10.808 24835 Z= 0.305 Chirality : 0.044 0.144 2753 Planarity : 0.004 0.046 3174 Dihedral : 7.089 98.075 2380 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2117 helix: 0.31 (0.32), residues: 264 sheet: 0.30 (0.22), residues: 561 loop : -0.20 (0.17), residues: 1292 =============================================================================== Job complete usr+sys time: 10493.54 seconds wall clock time: 185 minutes 14.95 seconds (11114.95 seconds total)