Starting phenix.real_space_refine on Tue Feb 20 00:18:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn4_30416/02_2024/7cn4_30416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn4_30416/02_2024/7cn4_30416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn4_30416/02_2024/7cn4_30416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn4_30416/02_2024/7cn4_30416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn4_30416/02_2024/7cn4_30416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn4_30416/02_2024/7cn4_30416.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16665 2.51 5 N 4341 2.21 5 O 5133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A GLU 864": "OE1" <-> "OE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B ARG 811": "NH1" <-> "NH2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B ARG 979": "NH1" <-> "NH2" Residue "B GLU 984": "OE1" <-> "OE2" Residue "B ARG 991": "NH1" <-> "NH2" Residue "B ARG 1087": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C ARG 811": "NH1" <-> "NH2" Residue "C GLU 864": "OE1" <-> "OE2" Residue "C ARG 979": "NH1" <-> "NH2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1087": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26253 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8499 Classifications: {'peptide': 1120} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 54, 'TRANS': 1065} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8499 Classifications: {'peptide': 1120} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 54, 'TRANS': 1065} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 143 Chain: "C" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8499 Classifications: {'peptide': 1120} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 54, 'TRANS': 1065} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 143 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 12.67, per 1000 atoms: 0.48 Number of scatterers: 26253 At special positions: 0 Unit cell: (150.467, 135.312, 164.54, 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 114 16.00 O 5133 8.00 N 4341 7.00 C 16665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 713 " " NAG A1309 " - " ASN A1070 " " NAG A1310 " - " ASN A 30 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 797 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 713 " " NAG B1309 " - " ASN B 797 " " NAG B1310 " - " ASN B1070 " " NAG B1311 " - " ASN B 30 " " NAG B1312 " - " ASN B 61 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 713 " " NAG C1309 " - " ASN C 797 " " NAG C1310 " - " ASN C1070 " " NAG C1311 " - " ASN C 30 " " NAG C1312 " - " ASN C 61 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN B 234 " " NAG H 1 " - " ASN C 234 " " NAG I 1 " - " ASN B 165 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN C 165 " " NAG L 1 " - " ASN C 122 " Time building additional restraints: 8.95 Conformation dependent library (CDL) restraints added in 4.4 seconds 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6276 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 51 sheets defined 25.1% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.079A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.635A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.642A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.527A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.642A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 742 through 753 removed outlier: 3.626A pdb=" N LEU A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.957A pdb=" N GLN A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.916A pdb=" N ASN A 820 " --> pdb=" O ASP A 816 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 removed outlier: 3.658A pdb=" N GLY A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.790A pdb=" N ALA A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 905 removed outlier: 3.926A pdb=" N TYR A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.593A pdb=" N TYR A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 934 Processing helix chain 'A' and resid 940 through 961 removed outlier: 4.022A pdb=" N LEU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 946 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.560A pdb=" N ILE A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.169A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.078A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.642A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.528A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.641A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 742 through 753 removed outlier: 3.626A pdb=" N LEU B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.962A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.916A pdb=" N ASN B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 838 removed outlier: 3.658A pdb=" N GLY B 838 " --> pdb=" O GLY B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 849 Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 882 through 887 removed outlier: 3.791A pdb=" N ALA B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 905 removed outlier: 4.013A pdb=" N TYR B 900 " --> pdb=" O MET B 896 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.592A pdb=" N TYR B 913 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 934 Processing helix chain 'B' and resid 940 through 961 removed outlier: 4.022A pdb=" N LEU B 944 " --> pdb=" O ALA B 940 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 946 " --> pdb=" O GLY B 942 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 955 " --> pdb=" O ASN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.560A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.169A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.078A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.642A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.527A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.642A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 753 removed outlier: 3.626A pdb=" N LEU C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.982A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.916A pdb=" N ASN C 820 " --> pdb=" O ASP C 816 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 838 removed outlier: 3.658A pdb=" N GLY C 838 " --> pdb=" O GLY C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 849 Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 882 through 887 removed outlier: 3.790A pdb=" N ALA C 886 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.200A pdb=" N TYR C 900 " --> pdb=" O MET C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.592A pdb=" N TYR C 913 " --> pdb=" O GLN C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 934 Processing helix chain 'C' and resid 940 through 961 removed outlier: 4.022A pdb=" N LEU C 944 " --> pdb=" O ALA C 940 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 946 " --> pdb=" O GLY C 942 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.560A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.169A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C1017 " --> pdb=" O GLU C1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.696A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.282A pdb=" N SER A 221 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.443A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.639A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.226A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.175A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.572A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 380 removed outlier: 4.133A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 542 removed outlier: 3.528A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.591A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 697 through 700 Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 710 removed outlier: 4.195A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 3.618A pdb=" N SER A 717 " --> pdb=" O THR A1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.601A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 786 removed outlier: 5.859A pdb=" N ILE A 784 " --> pdb=" O ASN B 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.697A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.282A pdb=" N SER B 221 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.443A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.639A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.227A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.175A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.572A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 376 through 380 removed outlier: 4.132A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 539 through 542 removed outlier: 5.475A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 707 through 710 removed outlier: 4.195A pdb=" N THR B1072 " --> pdb=" O SER B1093 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 724 removed outlier: 3.618A pdb=" N SER B 717 " --> pdb=" O THR B1062 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.601A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 783 through 786 removed outlier: 5.837A pdb=" N ILE B 784 " --> pdb=" O ASN C 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.696A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 33 through 36 removed outlier: 6.282A pdb=" N SER C 221 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.443A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.639A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.226A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.573A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 376 through 380 removed outlier: 4.132A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 539 through 542 removed outlier: 5.475A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 707 through 710 removed outlier: 4.195A pdb=" N THR C1072 " --> pdb=" O SER C1093 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 724 removed outlier: 3.618A pdb=" N SER C 717 " --> pdb=" O THR C1062 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.601A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1077 through 1079 998 hydrogen bonds defined for protein. 2673 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: 11.23 Time building geometry restraints manager: 9.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8231 1.34 - 1.46: 6576 1.46 - 1.59: 11881 1.59 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 26826 Sorted by residual: bond pdb=" C GLN A1067 " pdb=" N GLU A1068 " ideal model delta sigma weight residual 1.332 1.489 -0.156 1.40e-02 5.10e+03 1.24e+02 bond pdb=" C PRO B 859 " pdb=" N LEU B 860 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.27e-02 6.20e+03 4.11e+01 bond pdb=" C PRO A 859 " pdb=" N LEU A 860 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.27e-02 6.20e+03 4.09e+01 bond pdb=" C ALA A1066 " pdb=" N GLN A1067 " ideal model delta sigma weight residual 1.332 1.276 0.056 1.40e-02 5.10e+03 1.63e+01 bond pdb=" C LEU B 860 " pdb=" N LEU B 861 " ideal model delta sigma weight residual 1.331 1.273 0.057 1.42e-02 4.96e+03 1.62e+01 ... (remaining 26821 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 781 106.85 - 113.63: 14970 113.63 - 120.42: 9841 120.42 - 127.20: 10777 127.20 - 133.98: 213 Bond angle restraints: 36582 Sorted by residual: angle pdb=" N PRO C 251 " pdb=" CA PRO C 251 " pdb=" CB PRO C 251 " ideal model delta sigma weight residual 103.25 110.81 -7.56 1.05e+00 9.07e-01 5.18e+01 angle pdb=" N PRO A 251 " pdb=" CA PRO A 251 " pdb=" CB PRO A 251 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.17e+01 angle pdb=" N PRO B 251 " pdb=" CA PRO B 251 " pdb=" CB PRO B 251 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.16e+01 angle pdb=" CA ALA A1066 " pdb=" C ALA A1066 " pdb=" N GLN A1067 " ideal model delta sigma weight residual 116.05 122.85 -6.80 1.19e+00 7.06e-01 3.26e+01 angle pdb=" N ILE A 569 " pdb=" CA ILE A 569 " pdb=" C ILE A 569 " ideal model delta sigma weight residual 110.62 104.84 5.78 1.02e+00 9.61e-01 3.22e+01 ... (remaining 36577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.02: 15455 20.02 - 40.04: 972 40.04 - 60.05: 191 60.05 - 80.07: 41 80.07 - 100.09: 30 Dihedral angle restraints: 16689 sinusoidal: 6918 harmonic: 9771 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -174.13 88.13 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -174.12 88.12 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -174.12 88.12 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 16686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4231 0.133 - 0.266: 112 0.266 - 0.399: 11 0.399 - 0.532: 3 0.532 - 0.666: 2 Chirality restraints: 4359 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.75e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.55e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.09e+01 ... (remaining 4356 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.325 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG L 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.324 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG E 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " -0.309 2.00e-02 2.50e+03 2.71e-01 9.20e+02 pdb=" C7 NAG C1309 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " -0.159 2.00e-02 2.50e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 12 1.87 - 2.63: 295 2.63 - 3.39: 33045 3.39 - 4.14: 62719 4.14 - 4.90: 115002 Nonbonded interactions: 211073 Sorted by model distance: nonbonded pdb=" NH2 ARG B1015 " pdb=" OE1 GLU C1013 " model vdw 1.117 2.520 nonbonded pdb=" NH2 ARG A1015 " pdb=" OE1 GLU B1013 " model vdw 1.123 2.520 nonbonded pdb=" OE1 GLU A1013 " pdb=" NH2 ARG C1015 " model vdw 1.125 2.520 nonbonded pdb=" NH2 ARG B1015 " pdb=" CD GLU C1013 " model vdw 1.185 3.350 nonbonded pdb=" NH2 ARG A1015 " pdb=" CD GLU B1013 " model vdw 1.190 3.350 ... (remaining 211068 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.250 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: 6.800 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 64.850 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.230 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.006 0.156 26826 Z= 0.432 Angle : 0.803 8.754 36582 Z= 0.506 Chirality : 0.060 0.666 4359 Planarity : 0.012 0.283 4698 Dihedral : 14.357 100.090 10278 Min Nonbonded Distance : 1.117 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.95 % Favored : 92.70 % Rotamer: Outliers : 1.32 % Allowed : 4.23 % Favored : 94.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.12), residues: 3354 helix: -2.44 (0.16), residues: 657 sheet: -1.39 (0.17), residues: 696 loop : -2.69 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 882 HIS 0.002 0.001 HIS B1079 PHE 0.016 0.002 PHE C 902 TYR 0.013 0.001 TYR B 423 ARG 0.004 0.000 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 2.919 Fit side-chains revert: symmetry clash REVERT: A 900 TYR cc_start: 0.6846 (t80) cc_final: 0.6576 (t80) REVERT: A 1046 MET cc_start: 0.8513 (ptm) cc_final: 0.8261 (ptm) REVERT: B 900 TYR cc_start: 0.6741 (t80) cc_final: 0.6481 (t80) outliers start: 36 outliers final: 1 residues processed: 207 average time/residue: 1.3666 time to fit residues: 331.4612 Evaluate side-chains 103 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 800 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 4.9990 chunk 254 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 chunk 263 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 305 optimal weight: 10.0000 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 125 ASN A 137 ASN A 314 GLN A 360 ASN A 409 GLN A 540 ASN A 897 GLN A 921 ASN A 951 ASN A 961 GLN A 974 ASN B 121 ASN B 137 ASN B 314 GLN B 409 GLN B 540 ASN B 760 ASN B 800 GLN B 897 GLN B 921 ASN B 951 ASN B 961 GLN B 974 ASN C 137 ASN C 314 GLN C 360 ASN C 409 GLN C 760 ASN C 897 GLN C 909 GLN C 921 ASN C 951 ASN C 961 GLN C 974 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26826 Z= 0.207 Angle : 0.605 9.929 36582 Z= 0.318 Chirality : 0.046 0.263 4359 Planarity : 0.004 0.049 4698 Dihedral : 9.667 89.631 4734 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.40 % Allowed : 7.98 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 3354 helix: -0.69 (0.19), residues: 708 sheet: -0.88 (0.18), residues: 672 loop : -2.31 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 882 HIS 0.002 0.000 HIS C1079 PHE 0.011 0.001 PHE B 923 TYR 0.014 0.001 TYR A 495 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 3.393 Fit side-chains REVERT: A 1046 MET cc_start: 0.8475 (ptm) cc_final: 0.8272 (ptm) outliers start: 38 outliers final: 7 residues processed: 147 average time/residue: 1.2324 time to fit residues: 217.3283 Evaluate side-chains 105 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 305 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 760 ASN A 909 GLN B 800 GLN B 909 GLN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26826 Z= 0.238 Angle : 0.575 9.253 36582 Z= 0.300 Chirality : 0.046 0.241 4359 Planarity : 0.004 0.045 4698 Dihedral : 8.606 75.839 4731 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.51 % Allowed : 9.75 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3354 helix: 0.29 (0.20), residues: 708 sheet: -0.42 (0.19), residues: 648 loop : -2.09 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 882 HIS 0.002 0.000 HIS A1060 PHE 0.027 0.001 PHE B 157 TYR 0.017 0.001 TYR B 900 ARG 0.008 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 2.987 Fit side-chains revert: symmetry clash REVERT: A 1046 MET cc_start: 0.8425 (ptm) cc_final: 0.8186 (ptm) REVERT: B 131 CYS cc_start: 0.5368 (OUTLIER) cc_final: 0.4967 (m) outliers start: 41 outliers final: 18 residues processed: 143 average time/residue: 1.1664 time to fit residues: 201.8246 Evaluate side-chains 119 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 0.0030 chunk 324 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 360 ASN B 99 ASN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 211 ASN C 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 26826 Z= 0.407 Angle : 0.629 9.957 36582 Z= 0.326 Chirality : 0.048 0.247 4359 Planarity : 0.004 0.047 4698 Dihedral : 8.177 60.475 4731 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.80 % Allowed : 11.59 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3354 helix: 0.63 (0.20), residues: 690 sheet: -0.41 (0.19), residues: 681 loop : -1.97 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 882 HIS 0.003 0.001 HIS A1060 PHE 0.017 0.002 PHE C 902 TYR 0.014 0.001 TYR C 423 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 102 time to evaluate : 3.031 Fit side-chains REVERT: A 1046 MET cc_start: 0.8468 (ptm) cc_final: 0.8186 (ptm) REVERT: B 131 CYS cc_start: 0.5457 (OUTLIER) cc_final: 0.4985 (m) REVERT: B 1104 ASN cc_start: 0.8113 (m-40) cc_final: 0.7906 (m110) REVERT: C 131 CYS cc_start: 0.5357 (OUTLIER) cc_final: 0.4810 (m) outliers start: 49 outliers final: 28 residues processed: 141 average time/residue: 1.0282 time to fit residues: 177.6016 Evaluate side-chains 120 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1131 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 291 optimal weight: 7.9990 chunk 81 optimal weight: 0.4980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 121 ASN B 951 ASN C 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26826 Z= 0.267 Angle : 0.582 9.328 36582 Z= 0.300 Chirality : 0.046 0.239 4359 Planarity : 0.004 0.047 4698 Dihedral : 7.696 59.872 4731 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.91 % Allowed : 11.96 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3354 helix: 0.85 (0.20), residues: 708 sheet: -0.37 (0.19), residues: 693 loop : -1.88 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 PHE 0.031 0.001 PHE A 157 TYR 0.013 0.001 TYR A 495 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 102 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1046 MET cc_start: 0.8428 (ptm) cc_final: 0.8126 (ptm) outliers start: 52 outliers final: 29 residues processed: 144 average time/residue: 1.0625 time to fit residues: 187.4295 Evaluate side-chains 124 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 4.9990 chunk 292 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 190 optimal weight: 0.0970 chunk 80 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26826 Z= 0.184 Angle : 0.555 9.422 36582 Z= 0.285 Chirality : 0.045 0.238 4359 Planarity : 0.004 0.047 4698 Dihedral : 7.248 59.602 4731 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.51 % Allowed : 13.02 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3354 helix: 1.02 (0.20), residues: 711 sheet: -0.21 (0.20), residues: 663 loop : -1.79 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 882 HIS 0.001 0.000 HIS A1079 PHE 0.012 0.001 PHE A1085 TYR 0.012 0.001 TYR A 495 ARG 0.007 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1046 MET cc_start: 0.8373 (ptm) cc_final: 0.8076 (ptm) outliers start: 41 outliers final: 27 residues processed: 141 average time/residue: 1.1792 time to fit residues: 201.9256 Evaluate side-chains 124 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1131 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 237 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 273 optimal weight: 0.0980 chunk 181 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 360 ASN B1104 ASN C 360 ASN C 800 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26826 Z= 0.227 Angle : 0.560 9.422 36582 Z= 0.287 Chirality : 0.045 0.240 4359 Planarity : 0.004 0.045 4698 Dihedral : 7.058 59.742 4731 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.69 % Allowed : 13.36 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3354 helix: 1.16 (0.20), residues: 693 sheet: -0.10 (0.20), residues: 663 loop : -1.73 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 PHE 0.031 0.001 PHE A 157 TYR 0.012 0.001 TYR A 495 ARG 0.006 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 99 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1046 MET cc_start: 0.8393 (ptm) cc_final: 0.8120 (ptm) outliers start: 46 outliers final: 29 residues processed: 137 average time/residue: 1.0628 time to fit residues: 179.9940 Evaluate side-chains 124 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1131 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1131 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26826 Z= 0.237 Angle : 0.561 9.410 36582 Z= 0.289 Chirality : 0.045 0.240 4359 Planarity : 0.004 0.047 4698 Dihedral : 6.945 59.967 4731 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.73 % Allowed : 13.43 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3354 helix: 1.22 (0.20), residues: 693 sheet: -0.08 (0.20), residues: 663 loop : -1.70 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 PHE 0.012 0.001 PHE A1085 TYR 0.011 0.001 TYR A 495 ARG 0.006 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 99 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1001 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: A 1046 MET cc_start: 0.8372 (ptm) cc_final: 0.8069 (ptm) outliers start: 47 outliers final: 29 residues processed: 138 average time/residue: 1.0374 time to fit residues: 176.5030 Evaluate side-chains 123 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1131 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1131 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 HIS C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 26826 Z= 0.384 Angle : 0.618 9.415 36582 Z= 0.319 Chirality : 0.047 0.240 4359 Planarity : 0.004 0.045 4698 Dihedral : 7.086 58.212 4731 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.47 % Allowed : 13.83 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3354 helix: 1.10 (0.20), residues: 693 sheet: -0.24 (0.20), residues: 693 loop : -1.69 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 882 HIS 0.003 0.001 HIS A1060 PHE 0.034 0.001 PHE A 157 TYR 0.015 0.001 TYR A 900 ARG 0.008 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1046 MET cc_start: 0.8424 (ptm) cc_final: 0.8119 (ptm) outliers start: 40 outliers final: 30 residues processed: 129 average time/residue: 1.1433 time to fit residues: 180.4558 Evaluate side-chains 125 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1131 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.0770 chunk 319 optimal weight: 3.9990 chunk 194 optimal weight: 0.0040 chunk 151 optimal weight: 0.0870 chunk 221 optimal weight: 0.4980 chunk 334 optimal weight: 7.9990 chunk 308 optimal weight: 0.5980 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 163 optimal weight: 0.1980 overall best weight: 0.1728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26826 Z= 0.143 Angle : 0.546 9.471 36582 Z= 0.280 Chirality : 0.045 0.240 4359 Planarity : 0.004 0.047 4698 Dihedral : 6.568 58.975 4731 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.03 % Allowed : 14.31 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3354 helix: 1.28 (0.20), residues: 693 sheet: 0.03 (0.20), residues: 660 loop : -1.62 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 882 HIS 0.003 0.001 HIS A1044 PHE 0.013 0.001 PHE A1085 TYR 0.014 0.001 TYR B 495 ARG 0.012 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1046 MET cc_start: 0.8288 (ptm) cc_final: 0.8043 (ptm) outliers start: 28 outliers final: 19 residues processed: 130 average time/residue: 1.2510 time to fit residues: 197.9046 Evaluate side-chains 117 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 800 GLN B1104 ASN C 360 ASN C 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.056944 restraints weight = 62430.095| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.16 r_work: 0.2711 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26826 Z= 0.221 Angle : 0.555 9.492 36582 Z= 0.285 Chirality : 0.045 0.240 4359 Planarity : 0.004 0.064 4698 Dihedral : 6.615 58.961 4731 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.85 % Allowed : 14.86 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3354 helix: 1.31 (0.21), residues: 693 sheet: 0.05 (0.20), residues: 639 loop : -1.57 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 882 HIS 0.001 0.000 HIS C1084 PHE 0.033 0.001 PHE A 157 TYR 0.016 0.001 TYR C 900 ARG 0.014 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5315.66 seconds wall clock time: 101 minutes 56.31 seconds (6116.31 seconds total)