Starting phenix.real_space_refine on Mon Dec 11 13:08:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/12_2023/7uaf_26423_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/12_2023/7uaf_26423.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/12_2023/7uaf_26423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/12_2023/7uaf_26423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/12_2023/7uaf_26423_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/12_2023/7uaf_26423_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-1.21rc1-5172/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.81, per 1000 atoms: 0.55 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: 7.91 Conformation dependent library (CDL) restraints added in 3.4 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: 3.93 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: 5.68 Time building geometry restraints manager: 8.49 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=" 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 bond pdb=" C ASP C 385 " pdb=" N HIS C 386 " ideal model delta sigma weight residual 1.332 1.263 0.070 1.29e-02 6.01e+03 2.93e+01 bond pdb=" C ASP B 385 " pdb=" N HIS B 386 " ideal model delta sigma weight residual 1.332 1.279 0.054 1.29e-02 6.01e+03 1.74e+01 bond pdb=" C VAL D 300 " pdb=" N ASP D 301 " ideal model delta sigma weight residual 1.330 1.387 -0.057 1.38e-02 5.25e+03 1.72e+01 bond pdb=" C ARG B 579 " pdb=" N SER B 580 " ideal model delta sigma weight residual 1.330 1.272 0.058 1.52e-02 4.33e+03 1.47e+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 - 17.90: 10342 17.90 - 35.80: 698 35.80 - 53.70: 103 53.70 - 71.61: 49 71.61 - 89.51: 18 Dihedral angle restraints: 11210 sinusoidal: 5018 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 11207 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: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 3.400 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 53.990 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.000 ------------------------------------------------------------------------------- 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 0.082 18301 Z= 0.784 Angle : 1.800 8.822 24835 Z= 1.212 Chirality : 0.105 0.436 2753 Planarity : 0.021 0.275 3174 Dihedral : 13.074 89.507 7171 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 % Allowed : 3.11 % Favored : 96.73 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.138 0.022 TRP A 436 HIS 0.024 0.004 HIS C 573 PHE 0.073 0.012 PHE B 593 TYR 0.105 0.018 TYR A 313 ARG 0.010 0.001 ARG D 549 *********************** 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 : 2.071 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: 1.3653 time to fit residues: 857.6099 Evaluate side-chains 466 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 2.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8396 ------------------------------------------------------------------------------- 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: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18301 Z= 0.207 Angle : 0.611 8.873 24835 Z= 0.330 Chirality : 0.046 0.173 2753 Planarity : 0.003 0.030 3174 Dihedral : 6.646 51.503 3142 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.37 % Allowed : 10.61 % Favored : 87.02 % 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: -0.19 (0.31), residues: 264 sheet: 0.47 (0.20), residues: 573 loop : 0.26 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 361 HIS 0.012 0.001 HIS B 155 PHE 0.020 0.002 PHE C 245 TYR 0.019 0.001 TYR D 97 ARG 0.007 0.001 ARG D 74 *********************** 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 519 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 474 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 494 average time/residue: 1.4198 time to fit residues: 777.8984 Evaluate side-chains 479 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 462 time to evaluate : 2.021 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 9 average time/residue: 0.5142 time to fit residues: 8.7079 ------------------------------------------------------------------------------- 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: 5.9990 chunk 159 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 292 GLN D 341 GLN D 370 ASN D 558 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 18301 Z= 0.464 Angle : 0.664 8.024 24835 Z= 0.357 Chirality : 0.049 0.166 2753 Planarity : 0.004 0.064 3174 Dihedral : 6.175 40.845 3142 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.48 % Allowed : 13.40 % Favored : 83.11 % 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: 0.09 (0.18), residues: 2117 helix: -0.12 (0.31), residues: 264 sheet: 0.43 (0.21), residues: 584 loop : 0.02 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 361 HIS 0.011 0.002 HIS C 573 PHE 0.026 0.003 PHE B 593 TYR 0.021 0.002 TYR D 175 ARG 0.007 0.001 ARG D 579 *********************** 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 553 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 487 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 40 residues processed: 513 average time/residue: 1.3863 time to fit residues: 794.2746 Evaluate side-chains 513 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 473 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 17 residues processed: 24 average time/residue: 0.5217 time to fit residues: 19.1895 ------------------------------------------------------------------------------- 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: 0.7980 chunk 144 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 392 HIS B 443 GLN B 574 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7593 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18301 Z= 0.195 Angle : 0.543 6.823 24835 Z= 0.292 Chirality : 0.043 0.157 2753 Planarity : 0.003 0.039 3174 Dihedral : 5.632 43.138 3142 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.17 % Allowed : 15.94 % Favored : 80.90 % 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: 0.12 (0.18), residues: 2117 helix: 0.24 (0.32), residues: 264 sheet: 0.38 (0.21), residues: 573 loop : -0.00 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 361 HIS 0.007 0.001 HIS B 268 PHE 0.017 0.001 PHE A 245 TYR 0.026 0.001 TYR D 175 ARG 0.006 0.000 ARG D 579 *********************** 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 539 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 479 time to evaluate : 2.146 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: 34 residues processed: 505 average time/residue: 1.3869 time to fit residues: 779.3469 Evaluate side-chains 499 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 465 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 18 residues processed: 19 average time/residue: 0.3489 time to fit residues: 12.1056 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 370 ASN B 443 GLN B 574 GLN A 66 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 18301 Z= 0.615 Angle : 0.712 8.324 24835 Z= 0.380 Chirality : 0.052 0.193 2753 Planarity : 0.005 0.053 3174 Dihedral : 6.079 43.026 3142 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.43 % Allowed : 16.04 % Favored : 79.53 % 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: -0.27 (0.17), residues: 2117 helix: -0.24 (0.31), residues: 264 sheet: 0.23 (0.21), residues: 575 loop : -0.29 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 361 HIS 0.011 0.002 HIS B 155 PHE 0.024 0.003 PHE C 527 TYR 0.022 0.003 TYR D 175 ARG 0.009 0.001 ARG B 357 *********************** 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 560 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 476 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 42 residues processed: 519 average time/residue: 1.3667 time to fit residues: 789.9405 Evaluate side-chains 517 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 475 time to evaluate : 2.213 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 20 residues processed: 23 average time/residue: 0.4950 time to fit residues: 17.7564 ------------------------------------------------------------------------------- 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: 0.3980 chunk 183 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 16 optimal weight: 0.0050 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 474 ASN C 189 HIS C 215 GLN C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18301 Z= 0.175 Angle : 0.537 8.439 24835 Z= 0.289 Chirality : 0.043 0.144 2753 Planarity : 0.004 0.079 3174 Dihedral : 5.548 46.285 3142 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.96 % Allowed : 18.31 % Favored : 78.73 % 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: 0.01 (0.18), residues: 2117 helix: 0.25 (0.32), residues: 264 sheet: 0.38 (0.22), residues: 551 loop : -0.15 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 361 HIS 0.009 0.001 HIS B 268 PHE 0.022 0.001 PHE A 245 TYR 0.015 0.001 TYR D 175 ARG 0.018 0.000 ARG C 579 *********************** 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 528 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 472 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 31 residues processed: 504 average time/residue: 1.4079 time to fit residues: 790.6942 Evaluate side-chains 493 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 462 time to evaluate : 2.335 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 11 average time/residue: 0.6910 time to fit residues: 11.9926 ------------------------------------------------------------------------------- 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: 0.0470 chunk 116 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 203 optimal weight: 0.1980 chunk 127 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- 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 215 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN C 182 GLN 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: 0.7593 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18301 Z= 0.204 Angle : 0.529 7.736 24835 Z= 0.285 Chirality : 0.043 0.140 2753 Planarity : 0.004 0.049 3174 Dihedral : 5.375 46.527 3142 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.17 % Allowed : 18.42 % Favored : 78.42 % 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: 0.10 (0.18), residues: 2117 helix: 0.39 (0.33), residues: 264 sheet: 0.46 (0.22), residues: 549 loop : -0.11 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 361 HIS 0.009 0.001 HIS B 268 PHE 0.021 0.001 PHE A 245 TYR 0.013 0.001 TYR C 420 ARG 0.010 0.000 ARG C 69 *********************** 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 529 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 469 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 40 residues processed: 499 average time/residue: 1.4168 time to fit residues: 784.8297 Evaluate side-chains 504 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 464 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 21 residues processed: 20 average time/residue: 0.5076 time to fit residues: 15.7919 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- 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 268 HIS B 370 ASN B 443 GLN B 574 GLN A 573 HIS C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18301 Z= 0.290 Angle : 0.565 7.293 24835 Z= 0.303 Chirality : 0.044 0.141 2753 Planarity : 0.004 0.052 3174 Dihedral : 5.489 46.831 3142 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.74 % Allowed : 19.37 % Favored : 77.89 % 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: 0.28 (0.32), residues: 264 sheet: 0.42 (0.22), residues: 549 loop : -0.18 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 361 HIS 0.011 0.001 HIS B 268 PHE 0.025 0.002 PHE A 245 TYR 0.015 0.002 TYR A 472 ARG 0.008 0.000 ARG C 579 *********************** 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 517 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 465 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 40 residues processed: 491 average time/residue: 1.3618 time to fit residues: 742.7707 Evaluate side-chains 498 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 458 time to evaluate : 2.113 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 23 residues processed: 18 average time/residue: 0.7156 time to fit residues: 18.3482 ------------------------------------------------------------------------------- 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: 0.9990 chunk 177 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 179 optimal weight: 0.0570 chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN 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 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 341 GLN D 558 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18301 Z= 0.186 Angle : 0.523 8.103 24835 Z= 0.281 Chirality : 0.042 0.144 2753 Planarity : 0.004 0.049 3174 Dihedral : 5.326 46.731 3142 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.95 % Allowed : 20.26 % Favored : 77.78 % 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: 0.03 (0.18), residues: 2117 helix: 0.41 (0.33), residues: 265 sheet: 0.38 (0.22), residues: 565 loop : -0.16 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 361 HIS 0.011 0.001 HIS B 268 PHE 0.026 0.001 PHE A 245 TYR 0.013 0.001 TYR A 472 ARG 0.008 0.000 ARG C 579 *********************** 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 505 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 468 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 30 residues processed: 494 average time/residue: 1.3923 time to fit residues: 765.2598 Evaluate side-chains 489 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 459 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 7 average time/residue: 0.9438 time to fit residues: 10.2137 ------------------------------------------------------------------------------- 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: 5.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 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 D 519 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18301 Z= 0.287 Angle : 0.573 11.875 24835 Z= 0.305 Chirality : 0.044 0.141 2753 Planarity : 0.004 0.048 3174 Dihedral : 5.468 46.458 3142 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.01 % Allowed : 20.32 % Favored : 77.68 % 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: -0.03 (0.18), residues: 2117 helix: 0.31 (0.32), residues: 264 sheet: 0.42 (0.22), residues: 542 loop : -0.22 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 361 HIS 0.012 0.001 HIS B 268 PHE 0.017 0.002 PHE C 527 TYR 0.017 0.002 TYR A 472 ARG 0.008 0.000 ARG C 579 ********************** 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 498 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 460 time to evaluate : 2.067 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: 488 average time/residue: 1.4210 time to fit residues: 769.6044 Evaluate side-chains 496 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 461 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 11 average time/residue: 0.8466 time to fit residues: 14.0127 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 0.0980 chunk 154 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 165 HIS B 268 HIS B 370 ASN B 443 GLN B 574 GLN C 139 GLN C 177 ASN C 182 GLN C 189 HIS C 215 GLN C 574 GLN D 341 GLN D 558 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117341 restraints weight = 22372.332| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.72 r_work: 0.3435 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18301 Z= 0.361 Angle : 0.612 10.706 24835 Z= 0.326 Chirality : 0.046 0.146 2753 Planarity : 0.004 0.049 3174 Dihedral : 5.685 46.820 3142 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.11 % Allowed : 20.37 % Favored : 77.52 % 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: -0.20 (0.18), residues: 2117 helix: 0.18 (0.32), residues: 264 sheet: 0.25 (0.22), residues: 553 loop : -0.31 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 361 HIS 0.013 0.002 HIS B 268 PHE 0.026 0.002 PHE A 245 TYR 0.018 0.002 TYR A 472 ARG 0.007 0.001 ARG C 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10766.98 seconds wall clock time: 189 minutes 36.15 seconds (11376.15 seconds total)