Starting phenix.real_space_refine on Wed Feb 21 18:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ni2_12349/02_2024/7ni2_12349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ni2_12349/02_2024/7ni2_12349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ni2_12349/02_2024/7ni2_12349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ni2_12349/02_2024/7ni2_12349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ni2_12349/02_2024/7ni2_12349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ni2_12349/02_2024/7ni2_12349.pdb" } resolution = 2.89 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= 0.008 sd= 0.060 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 20088 2.51 5 N 5264 2.21 5 O 5888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C GLU 626": "OE1" <-> "OE2" Residue "C TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 224": "OD1" <-> "OD2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D GLU 626": "OE1" <-> "OE2" Residue "D TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 224": "OD1" <-> "OD2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "E GLU 600": "OE1" <-> "OE2" Residue "E GLU 626": "OE1" <-> "OE2" Residue "E TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 224": "OD1" <-> "OD2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "F GLU 600": "OE1" <-> "OE2" Residue "F GLU 626": "OE1" <-> "OE2" Residue "F TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 58": "OD1" <-> "OD2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 224": "OD1" <-> "OD2" Residue "G GLU 463": "OE1" <-> "OE2" Residue "G GLU 600": "OE1" <-> "OE2" Residue "G GLU 626": "OE1" <-> "OE2" Residue "G TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 224": "OD1" <-> "OD2" Residue "H GLU 463": "OE1" <-> "OE2" Residue "H GLU 600": "OE1" <-> "OE2" Residue "H GLU 626": "OE1" <-> "OE2" Residue "H TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Chain: "B" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Chain: "C" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Chain: "D" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Chain: "E" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Chain: "F" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Chain: "G" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Chain: "H" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Time building chain proxies: 16.84, per 1000 atoms: 0.54 Number of scatterers: 31344 At special positions: 0 Unit cell: (162.876, 162.045, 138.777, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 5888 8.00 N 5264 7.00 C 20088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 6.5 seconds 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 32 sheets defined 46.3% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 removed outlier: 3.581A pdb=" N LYS A 101 " --> pdb=" O MET A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 450 Processing helix chain 'A' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.638A pdb=" N MET A 522 " --> pdb=" O HIS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.696A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.039A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 450 Processing helix chain 'B' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET B 522 " --> pdb=" O HIS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 removed outlier: 3.579A pdb=" N LYS C 101 " --> pdb=" O MET C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.970A pdb=" N LEU C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 450 Processing helix chain 'C' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET C 522 " --> pdb=" O HIS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 555 removed outlier: 3.778A pdb=" N THR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 623 through 636 removed outlier: 3.559A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 4.037A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS D 101 " --> pdb=" O MET D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.970A pdb=" N LEU D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 450 Processing helix chain 'D' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET D 522 " --> pdb=" O HIS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY D 575 " --> pdb=" O HIS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 595' Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 623 through 636 removed outlier: 3.559A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS E 101 " --> pdb=" O MET E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 450 Processing helix chain 'E' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET E 522 " --> pdb=" O HIS E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR E 554 " --> pdb=" O THR E 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 575 removed outlier: 3.683A pdb=" N GLY E 575 " --> pdb=" O HIS E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 587 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.694A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 595' Processing helix chain 'E' and resid 615 through 621 Processing helix chain 'E' and resid 623 through 636 removed outlier: 3.559A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.581A pdb=" N LYS F 101 " --> pdb=" O MET F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 450 Processing helix chain 'F' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET F 522 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR F 554 " --> pdb=" O THR F 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY F 575 " --> pdb=" O HIS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 591 through 595' Processing helix chain 'F' and resid 615 through 621 Processing helix chain 'F' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.608A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS G 101 " --> pdb=" O MET G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 450 Processing helix chain 'G' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET G 522 " --> pdb=" O HIS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 555 removed outlier: 3.776A pdb=" N THR G 554 " --> pdb=" O THR G 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY G 575 " --> pdb=" O HIS G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 587 Processing helix chain 'G' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE G 595 " --> pdb=" O ALA G 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 595' Processing helix chain 'G' and resid 615 through 621 Processing helix chain 'G' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.608A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 4.037A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS H 101 " --> pdb=" O MET H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 removed outlier: 3.968A pdb=" N LEU H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 450 Processing helix chain 'H' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 522 removed outlier: 3.638A pdb=" N MET H 522 " --> pdb=" O HIS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR H 554 " --> pdb=" O THR H 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY H 555 " --> pdb=" O ILE H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY H 575 " --> pdb=" O HIS H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 587 Processing helix chain 'H' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE H 595 " --> pdb=" O ALA H 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 591 through 595' Processing helix chain 'H' and resid 615 through 621 Processing helix chain 'H' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.608A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP A 136 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 182 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 558 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 607 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 604 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 221 removed outlier: 7.080A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP B 136 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 182 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU B 695 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 471 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY B 697 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 558 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE B 607 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE B 560 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 604 " --> pdb=" O VAL B 599 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU C 60 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP C 136 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 182 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU C 695 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 471 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 697 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 558 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE C 607 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE C 560 " --> pdb=" O ILE C 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 604 " --> pdb=" O VAL C 599 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 221 removed outlier: 7.080A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP D 136 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 182 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL D 558 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE D 607 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 560 " --> pdb=" O ILE D 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE D 604 " --> pdb=" O VAL D 599 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 141 removed outlier: 3.613A pdb=" N ASP E 136 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 182 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU E 695 " --> pdb=" O TYR E 469 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER E 471 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY E 697 " --> pdb=" O SER E 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE E 604 " --> pdb=" O VAL E 599 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP F 136 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 182 " --> pdb=" O LEU F 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE F 604 " --> pdb=" O VAL F 599 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP G 136 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 182 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU G 695 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER G 471 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY G 697 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY G 533 " --> pdb=" O THR G 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE G 604 " --> pdb=" O VAL G 599 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP H 136 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 182 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU H 695 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER H 471 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY H 697 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL H 558 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE H 607 " --> pdb=" O VAL H 558 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE H 560 " --> pdb=" O ILE H 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE H 604 " --> pdb=" O VAL H 599 " (cutoff:3.500A) 1564 hydrogen bonds defined for protein. 4572 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: 11.31 Time building geometry restraints manager: 14.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10116 1.34 - 1.45: 3221 1.45 - 1.57: 18279 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 31808 Sorted by residual: bond pdb=" CB ASP H 642 " pdb=" CG ASP H 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.47e+00 bond pdb=" CB ASP G 642 " pdb=" CG ASP G 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.46e+00 bond pdb=" CB ASP B 642 " pdb=" CG ASP B 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.46e+00 bond pdb=" CB ASP D 642 " pdb=" CG ASP D 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.45e+00 bond pdb=" CB ASP A 642 " pdb=" CG ASP A 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.45e+00 ... (remaining 31803 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.73: 659 105.73 - 112.78: 17858 112.78 - 119.84: 10211 119.84 - 126.90: 14113 126.90 - 133.95: 263 Bond angle restraints: 43104 Sorted by residual: angle pdb=" CB MET F 540 " pdb=" CG MET F 540 " pdb=" SD MET F 540 " ideal model delta sigma weight residual 112.70 104.27 8.43 3.00e+00 1.11e-01 7.90e+00 angle pdb=" CB MET B 540 " pdb=" CG MET B 540 " pdb=" SD MET B 540 " ideal model delta sigma weight residual 112.70 104.28 8.42 3.00e+00 1.11e-01 7.88e+00 angle pdb=" CB MET G 540 " pdb=" CG MET G 540 " pdb=" SD MET G 540 " ideal model delta sigma weight residual 112.70 104.28 8.42 3.00e+00 1.11e-01 7.87e+00 angle pdb=" CB MET A 540 " pdb=" CG MET A 540 " pdb=" SD MET A 540 " ideal model delta sigma weight residual 112.70 104.29 8.41 3.00e+00 1.11e-01 7.87e+00 angle pdb=" CB MET C 540 " pdb=" CG MET C 540 " pdb=" SD MET C 540 " ideal model delta sigma weight residual 112.70 104.29 8.41 3.00e+00 1.11e-01 7.87e+00 ... (remaining 43099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 18207 17.68 - 35.36: 1041 35.36 - 53.05: 104 53.05 - 70.73: 40 70.73 - 88.41: 16 Dihedral angle restraints: 19408 sinusoidal: 7712 harmonic: 11696 Sorted by residual: dihedral pdb=" CA HIS D 576 " pdb=" C HIS D 576 " pdb=" N LYS D 577 " pdb=" CA LYS D 577 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA HIS E 576 " pdb=" C HIS E 576 " pdb=" N LYS E 577 " pdb=" CA LYS E 577 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA HIS H 576 " pdb=" C HIS H 576 " pdb=" N LYS H 577 " pdb=" CA LYS H 577 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 19405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3301 0.041 - 0.082: 1424 0.082 - 0.123: 405 0.123 - 0.164: 67 0.164 - 0.206: 11 Chirality restraints: 5208 Sorted by residual: chirality pdb=" CB THR E 233 " pdb=" CA THR E 233 " pdb=" OG1 THR E 233 " pdb=" CG2 THR E 233 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR A 233 " pdb=" CA THR A 233 " pdb=" OG1 THR A 233 " pdb=" CG2 THR A 233 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB THR H 233 " pdb=" CA THR H 233 " pdb=" OG1 THR H 233 " pdb=" CG2 THR H 233 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 5205 not shown) Planarity restraints: 5480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 197 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO E 198 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 198 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 198 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 197 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO D 198 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 197 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO H 198 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO H 198 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 198 " 0.041 5.00e-02 4.00e+02 ... (remaining 5477 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3302 2.74 - 3.28: 33021 3.28 - 3.82: 51443 3.82 - 4.36: 62769 4.36 - 4.90: 106249 Nonbonded interactions: 256784 Sorted by model distance: nonbonded pdb=" OG SER G 86 " pdb=" OD2 ASP G 224 " model vdw 2.198 2.440 nonbonded pdb=" OG SER E 86 " pdb=" OD2 ASP E 224 " model vdw 2.199 2.440 nonbonded pdb=" OG SER F 86 " pdb=" OD2 ASP F 224 " model vdw 2.199 2.440 nonbonded pdb=" OG SER A 86 " pdb=" OD2 ASP A 224 " model vdw 2.199 2.440 nonbonded pdb=" OG SER D 86 " pdb=" OD2 ASP D 224 " model vdw 2.199 2.440 ... (remaining 256779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.640 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: 12.800 Check model and map are aligned: 0.450 Set scattering table: 0.310 Process input model: 84.030 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.190 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 31808 Z= 0.428 Angle : 0.696 9.336 43104 Z= 0.370 Chirality : 0.049 0.206 5208 Planarity : 0.005 0.076 5480 Dihedral : 11.383 88.410 11872 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4016 helix: -0.47 (0.12), residues: 1760 sheet: 0.09 (0.23), residues: 512 loop : -1.86 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 631 HIS 0.003 0.001 HIS G 518 PHE 0.031 0.003 PHE C 220 TYR 0.020 0.002 TYR A 165 ARG 0.018 0.001 ARG A 609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 4.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 127 LEU cc_start: 0.9218 (mt) cc_final: 0.8980 (mt) outliers start: 0 outliers final: 3 residues processed: 454 average time/residue: 1.2039 time to fit residues: 659.5258 Evaluate side-chains 344 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 341 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain H residue 192 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.8980 chunk 309 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 238 optimal weight: 0.8980 chunk 370 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 183 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 183 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 183 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN F 183 ASN ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN H 183 ASN ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31808 Z= 0.211 Angle : 0.612 9.342 43104 Z= 0.297 Chirality : 0.045 0.171 5208 Planarity : 0.004 0.041 5480 Dihedral : 4.524 27.673 4334 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.56 % Allowed : 9.67 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.66 (0.13), residues: 4016 helix: 0.35 (0.12), residues: 1800 sheet: 0.01 (0.18), residues: 720 loop : -1.58 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 631 HIS 0.005 0.001 HIS B 571 PHE 0.018 0.001 PHE H 220 TYR 0.014 0.001 TYR C 569 ARG 0.004 0.000 ARG H 609 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 399 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8684 (t0) cc_final: 0.8394 (p0) REVERT: A 707 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7323 (tmm160) REVERT: B 164 ASN cc_start: 0.8380 (t0) cc_final: 0.8151 (p0) REVERT: C 164 ASN cc_start: 0.8634 (t0) cc_final: 0.8403 (p0) REVERT: C 707 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7303 (tmm160) REVERT: D 164 ASN cc_start: 0.8488 (t0) cc_final: 0.8252 (p0) REVERT: E 164 ASN cc_start: 0.8389 (t0) cc_final: 0.8104 (p0) REVERT: G 127 LEU cc_start: 0.9223 (mt) cc_final: 0.9009 (mt) REVERT: G 164 ASN cc_start: 0.8544 (t0) cc_final: 0.8216 (p0) REVERT: H 451 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7324 (tt) REVERT: H 474 ILE cc_start: 0.9057 (tt) cc_final: 0.8828 (tp) outliers start: 54 outliers final: 18 residues processed: 428 average time/residue: 1.0162 time to fit residues: 546.8860 Evaluate side-chains 374 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 353 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 0.9980 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 192 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31808 Z= 0.292 Angle : 0.619 9.203 43104 Z= 0.302 Chirality : 0.046 0.198 5208 Planarity : 0.004 0.045 5480 Dihedral : 4.477 26.528 4328 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.57 % Allowed : 12.33 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4016 helix: 0.46 (0.12), residues: 1800 sheet: 0.20 (0.19), residues: 720 loop : -1.47 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 631 HIS 0.004 0.001 HIS B 571 PHE 0.018 0.002 PHE H 220 TYR 0.013 0.002 TYR D 141 ARG 0.004 0.000 ARG G 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 376 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8683 (t0) cc_final: 0.8433 (p0) REVERT: A 707 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7357 (tmm160) REVERT: B 680 MET cc_start: 0.8332 (mmm) cc_final: 0.8106 (mtt) REVERT: C 707 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7343 (tmm160) REVERT: D 103 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8646 (mp) REVERT: D 680 MET cc_start: 0.8324 (mmm) cc_final: 0.8096 (mtt) REVERT: E 164 ASN cc_start: 0.8405 (t0) cc_final: 0.8134 (p0) REVERT: F 103 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8595 (mp) REVERT: F 680 MET cc_start: 0.8357 (mmm) cc_final: 0.8107 (mtt) REVERT: G 127 LEU cc_start: 0.9200 (mt) cc_final: 0.8986 (mt) REVERT: G 164 ASN cc_start: 0.8561 (t0) cc_final: 0.8248 (p0) REVERT: H 451 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7412 (tt) REVERT: H 680 MET cc_start: 0.8317 (mmm) cc_final: 0.8097 (mtt) outliers start: 89 outliers final: 47 residues processed: 419 average time/residue: 1.1070 time to fit residues: 578.9795 Evaluate side-chains 391 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 339 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 445 VAL Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31808 Z= 0.267 Angle : 0.608 9.179 43104 Z= 0.295 Chirality : 0.046 0.168 5208 Planarity : 0.004 0.052 5480 Dihedral : 4.359 25.789 4328 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 13.97 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.36 (0.13), residues: 4016 helix: 0.56 (0.12), residues: 1800 sheet: 0.22 (0.19), residues: 720 loop : -1.40 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 631 HIS 0.003 0.001 HIS B 571 PHE 0.018 0.002 PHE C 574 TYR 0.012 0.001 TYR H 141 ARG 0.004 0.000 ARG E 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 359 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8685 (t0) cc_final: 0.8427 (p0) REVERT: A 221 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8416 (m) REVERT: A 707 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7324 (tmm160) REVERT: B 680 MET cc_start: 0.8279 (mmm) cc_final: 0.8068 (mtt) REVERT: C 221 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8420 (m) REVERT: C 451 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7487 (tt) REVERT: C 707 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7336 (tmm160) REVERT: D 103 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8638 (mp) REVERT: D 192 ASN cc_start: 0.8567 (m-40) cc_final: 0.8046 (p0) REVERT: D 680 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8063 (mtt) REVERT: E 164 ASN cc_start: 0.8473 (t0) cc_final: 0.8193 (p0) REVERT: F 127 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8511 (mm) REVERT: F 192 ASN cc_start: 0.8502 (m-40) cc_final: 0.8100 (p0) REVERT: F 680 MET cc_start: 0.8320 (mmm) cc_final: 0.8080 (mtt) REVERT: G 127 LEU cc_start: 0.9175 (mt) cc_final: 0.8969 (mt) REVERT: G 164 ASN cc_start: 0.8613 (t0) cc_final: 0.8309 (p0) REVERT: G 221 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8417 (m) REVERT: H 192 ASN cc_start: 0.8554 (m-40) cc_final: 0.8128 (p0) REVERT: H 451 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7409 (tt) REVERT: H 680 MET cc_start: 0.8295 (mmm) cc_final: 0.8094 (mtt) outliers start: 87 outliers final: 48 residues processed: 399 average time/residue: 0.9987 time to fit residues: 498.5777 Evaluate side-chains 397 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 339 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 445 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 0.7980 chunk 353 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31808 Z= 0.178 Angle : 0.584 9.311 43104 Z= 0.279 Chirality : 0.045 0.210 5208 Planarity : 0.004 0.049 5480 Dihedral : 4.068 24.129 4328 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.91 % Allowed : 15.96 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.22 (0.13), residues: 4016 helix: 0.82 (0.12), residues: 1784 sheet: -0.26 (0.19), residues: 816 loop : -1.23 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 631 HIS 0.003 0.001 HIS B 571 PHE 0.018 0.001 PHE B 574 TYR 0.013 0.001 TYR E 141 ARG 0.002 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 381 time to evaluate : 4.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8650 (t0) cc_final: 0.8390 (p0) REVERT: A 221 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8444 (m) REVERT: A 707 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7306 (tmm160) REVERT: B 221 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8443 (m) REVERT: C 127 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8533 (mm) REVERT: C 221 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8449 (m) REVERT: C 451 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7470 (tt) REVERT: C 707 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7288 (tmm160) REVERT: D 127 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8724 (mm) REVERT: D 192 ASN cc_start: 0.8438 (m-40) cc_final: 0.7946 (p0) REVERT: D 221 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8424 (m) REVERT: E 164 ASN cc_start: 0.8427 (t0) cc_final: 0.8190 (p0) REVERT: E 221 SER cc_start: 0.8660 (t) cc_final: 0.8432 (m) REVERT: F 127 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8495 (mm) REVERT: F 192 ASN cc_start: 0.8460 (m-40) cc_final: 0.8042 (p0) REVERT: F 221 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8426 (m) REVERT: F 680 MET cc_start: 0.8300 (mmm) cc_final: 0.8074 (mtt) REVERT: G 164 ASN cc_start: 0.8543 (t0) cc_final: 0.8311 (p0) REVERT: G 221 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (m) REVERT: G 451 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7473 (tt) REVERT: H 192 ASN cc_start: 0.8433 (m-40) cc_final: 0.7980 (p0) REVERT: H 221 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8413 (m) outliers start: 66 outliers final: 19 residues processed: 410 average time/residue: 1.0570 time to fit residues: 537.8096 Evaluate side-chains 379 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 346 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 4.9990 chunk 355 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31808 Z= 0.175 Angle : 0.595 9.968 43104 Z= 0.282 Chirality : 0.045 0.286 5208 Planarity : 0.004 0.049 5480 Dihedral : 3.971 23.066 4328 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.00 % Allowed : 16.48 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.13), residues: 4016 helix: 0.94 (0.12), residues: 1776 sheet: 0.07 (0.20), residues: 728 loop : -1.27 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 631 HIS 0.003 0.001 HIS H 571 PHE 0.011 0.001 PHE B 574 TYR 0.013 0.001 TYR F 141 ARG 0.002 0.000 ARG H 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 369 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8658 (t0) cc_final: 0.8404 (p0) REVERT: A 707 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7297 (tmm160) REVERT: B 451 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7324 (tt) REVERT: C 127 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8482 (mm) REVERT: C 192 ASN cc_start: 0.8640 (m-40) cc_final: 0.8031 (p0) REVERT: C 451 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (tt) REVERT: C 707 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7278 (tmm160) REVERT: D 127 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8731 (mm) REVERT: D 192 ASN cc_start: 0.8418 (m-40) cc_final: 0.7908 (p0) REVERT: D 260 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7961 (mp) REVERT: D 451 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7248 (tt) REVERT: E 164 ASN cc_start: 0.8423 (t0) cc_final: 0.8208 (p0) REVERT: E 221 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8454 (m) REVERT: E 414 ASN cc_start: 0.8362 (p0) cc_final: 0.8160 (p0) REVERT: F 127 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8566 (mm) REVERT: F 192 ASN cc_start: 0.8414 (m-40) cc_final: 0.7992 (p0) REVERT: F 451 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7430 (tt) REVERT: G 164 ASN cc_start: 0.8535 (t0) cc_final: 0.8309 (p0) REVERT: G 221 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (m) REVERT: G 451 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7459 (tt) REVERT: H 127 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8680 (mm) REVERT: H 192 ASN cc_start: 0.8387 (m-40) cc_final: 0.7935 (p0) REVERT: H 221 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8419 (m) REVERT: H 451 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7287 (tt) outliers start: 104 outliers final: 32 residues processed: 434 average time/residue: 1.0442 time to fit residues: 562.3102 Evaluate side-chains 390 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 342 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 573 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 445 VAL Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 224 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31808 Z= 0.172 Angle : 0.609 11.333 43104 Z= 0.288 Chirality : 0.046 0.328 5208 Planarity : 0.004 0.050 5480 Dihedral : 3.895 21.910 4328 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.11 % Allowed : 18.04 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.13), residues: 4016 helix: 1.19 (0.12), residues: 1728 sheet: 0.16 (0.20), residues: 728 loop : -1.10 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 631 HIS 0.003 0.001 HIS H 571 PHE 0.013 0.001 PHE F 574 TYR 0.014 0.001 TYR D 141 ARG 0.003 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 363 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8604 (t0) cc_final: 0.8348 (p0) REVERT: A 410 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7622 (ttp80) REVERT: A 414 ASN cc_start: 0.8382 (p0) cc_final: 0.8141 (p0) REVERT: A 707 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7293 (tmm160) REVERT: B 451 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7337 (tt) REVERT: C 127 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8546 (mm) REVERT: C 414 ASN cc_start: 0.8372 (p0) cc_final: 0.8129 (p0) REVERT: C 451 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7382 (tt) REVERT: C 707 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7276 (tmm160) REVERT: D 127 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8749 (mm) REVERT: D 192 ASN cc_start: 0.8376 (m-40) cc_final: 0.7873 (p0) REVERT: D 451 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7286 (tt) REVERT: E 164 ASN cc_start: 0.8409 (t0) cc_final: 0.8178 (p0) REVERT: E 414 ASN cc_start: 0.8337 (p0) cc_final: 0.8116 (p0) REVERT: F 127 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8618 (mm) REVERT: F 192 ASN cc_start: 0.8391 (m-40) cc_final: 0.7931 (p0) REVERT: F 451 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7420 (tt) REVERT: G 164 ASN cc_start: 0.8521 (t0) cc_final: 0.8294 (p0) REVERT: G 414 ASN cc_start: 0.8361 (p0) cc_final: 0.8133 (p0) REVERT: G 451 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7414 (tt) REVERT: H 127 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8723 (mm) REVERT: H 192 ASN cc_start: 0.8388 (m-40) cc_final: 0.7879 (p0) REVERT: H 451 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7281 (tt) outliers start: 73 outliers final: 34 residues processed: 414 average time/residue: 0.9991 time to fit residues: 517.9696 Evaluate side-chains 391 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 345 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 445 VAL Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 0.4980 chunk 118 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 chunk 267 optimal weight: 0.3980 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 309 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31808 Z= 0.140 Angle : 0.608 12.277 43104 Z= 0.283 Chirality : 0.046 0.345 5208 Planarity : 0.004 0.055 5480 Dihedral : 3.708 20.408 4328 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.76 % Allowed : 18.88 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.40 (0.13), residues: 4016 helix: 1.40 (0.13), residues: 1728 sheet: 0.28 (0.20), residues: 720 loop : -1.01 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 631 HIS 0.003 0.000 HIS H 571 PHE 0.011 0.001 PHE C 117 TYR 0.013 0.001 TYR F 141 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 377 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8505 (t0) cc_final: 0.8260 (p0) REVERT: A 410 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7629 (ttp80) REVERT: A 414 ASN cc_start: 0.8247 (p0) cc_final: 0.7994 (p0) REVERT: A 707 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7310 (tmm160) REVERT: B 451 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7324 (tt) REVERT: B 573 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7168 (ppp) REVERT: C 127 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8492 (mm) REVERT: C 414 ASN cc_start: 0.8219 (p0) cc_final: 0.7967 (p0) REVERT: C 451 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7346 (tt) REVERT: C 707 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7315 (tmm160) REVERT: D 192 ASN cc_start: 0.8371 (m-40) cc_final: 0.7811 (p0) REVERT: D 451 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7338 (tt) REVERT: E 414 ASN cc_start: 0.8213 (p0) cc_final: 0.7966 (p0) REVERT: F 127 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8651 (mm) REVERT: F 192 ASN cc_start: 0.8368 (m-40) cc_final: 0.7774 (m-40) REVERT: F 451 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7357 (tt) REVERT: G 164 ASN cc_start: 0.8462 (t0) cc_final: 0.8231 (p0) REVERT: G 414 ASN cc_start: 0.8244 (p0) cc_final: 0.7999 (p0) REVERT: G 451 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7358 (tt) REVERT: H 192 ASN cc_start: 0.8360 (m-40) cc_final: 0.7854 (p0) outliers start: 61 outliers final: 25 residues processed: 415 average time/residue: 1.0515 time to fit residues: 542.7904 Evaluate side-chains 383 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 348 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 573 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 2.9990 chunk 366 optimal weight: 8.9990 chunk 220 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 287 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 346 optimal weight: 0.5980 chunk 365 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31808 Z= 0.191 Angle : 0.636 13.031 43104 Z= 0.298 Chirality : 0.047 0.346 5208 Planarity : 0.004 0.054 5480 Dihedral : 3.824 19.757 4328 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.67 % Allowed : 19.49 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.41 (0.13), residues: 4016 helix: 1.37 (0.13), residues: 1728 sheet: 0.30 (0.20), residues: 720 loop : -0.95 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 631 HIS 0.003 0.001 HIS H 571 PHE 0.010 0.001 PHE H 117 TYR 0.017 0.001 TYR G 141 ARG 0.002 0.000 ARG G 566 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 370 time to evaluate : 3.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8507 (t0) cc_final: 0.8248 (p0) REVERT: A 414 ASN cc_start: 0.8258 (p0) cc_final: 0.7968 (p0) REVERT: A 707 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7282 (tmm160) REVERT: B 451 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7343 (tt) REVERT: C 127 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8453 (mm) REVERT: C 414 ASN cc_start: 0.8243 (p0) cc_final: 0.7951 (p0) REVERT: C 451 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7385 (tt) REVERT: C 707 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7285 (tmm160) REVERT: D 192 ASN cc_start: 0.8399 (m-40) cc_final: 0.7675 (m-40) REVERT: D 451 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7348 (tt) REVERT: D 573 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7210 (ppp) REVERT: E 414 ASN cc_start: 0.8243 (p0) cc_final: 0.7949 (p0) REVERT: F 127 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8655 (mm) REVERT: F 451 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7387 (tt) REVERT: F 573 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7163 (ppp) REVERT: G 164 ASN cc_start: 0.8474 (t0) cc_final: 0.8257 (p0) REVERT: G 414 ASN cc_start: 0.8246 (p0) cc_final: 0.7961 (p0) REVERT: G 451 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7350 (tt) REVERT: H 192 ASN cc_start: 0.8351 (m-40) cc_final: 0.7808 (p0) outliers start: 58 outliers final: 26 residues processed: 411 average time/residue: 1.0838 time to fit residues: 549.4758 Evaluate side-chains 393 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 356 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 3.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 183 optimal weight: 0.0170 chunk 269 optimal weight: 7.9990 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 9.9990 chunk 323 optimal weight: 0.0000 chunk 33 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31808 Z= 0.141 Angle : 0.634 14.102 43104 Z= 0.294 Chirality : 0.047 0.354 5208 Planarity : 0.004 0.063 5480 Dihedral : 3.658 18.920 4328 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.30 % Allowed : 20.27 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 4016 helix: 1.47 (0.13), residues: 1736 sheet: 0.32 (0.20), residues: 720 loop : -0.89 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 631 HIS 0.003 0.000 HIS H 571 PHE 0.011 0.001 PHE E 117 TYR 0.015 0.001 TYR C 141 ARG 0.004 0.000 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 374 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.8451 (t0) cc_final: 0.8173 (p0) REVERT: A 414 ASN cc_start: 0.8118 (p0) cc_final: 0.7833 (p0) REVERT: A 707 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (tmm160) REVERT: C 127 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8443 (mm) REVERT: C 414 ASN cc_start: 0.8099 (p0) cc_final: 0.7862 (p0) REVERT: C 451 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7337 (tt) REVERT: C 707 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7282 (tmm160) REVERT: E 164 ASN cc_start: 0.8298 (t0) cc_final: 0.8073 (p0) REVERT: E 414 ASN cc_start: 0.8087 (p0) cc_final: 0.7820 (p0) REVERT: F 127 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8676 (mm) REVERT: G 42 LEU cc_start: 0.8159 (tm) cc_final: 0.7959 (tt) REVERT: G 164 ASN cc_start: 0.8437 (t0) cc_final: 0.8224 (p0) REVERT: G 414 ASN cc_start: 0.8097 (p0) cc_final: 0.7816 (p0) REVERT: G 451 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7313 (tt) REVERT: H 192 ASN cc_start: 0.8326 (m-40) cc_final: 0.7670 (m-40) outliers start: 45 outliers final: 23 residues processed: 409 average time/residue: 1.1214 time to fit residues: 568.8107 Evaluate side-chains 383 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 chunk 99 optimal weight: 0.0570 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.160430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108322 restraints weight = 46948.673| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.38 r_work: 0.3253 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31808 Z= 0.164 Angle : 0.647 15.509 43104 Z= 0.299 Chirality : 0.048 0.371 5208 Planarity : 0.004 0.058 5480 Dihedral : 3.711 18.896 4328 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.10 % Allowed : 20.87 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.58 (0.13), residues: 4016 helix: 1.49 (0.13), residues: 1728 sheet: 0.40 (0.20), residues: 720 loop : -0.86 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 631 HIS 0.002 0.000 HIS H 571 PHE 0.010 0.001 PHE F 117 TYR 0.021 0.001 TYR E 141 ARG 0.003 0.000 ARG E 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10426.39 seconds wall clock time: 186 minutes 47.20 seconds (11207.20 seconds total)