Starting phenix.real_space_refine on Tue Mar 19 21:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/03_2024/7vhj_31996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/03_2024/7vhj_31996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/03_2024/7vhj_31996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/03_2024/7vhj_31996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/03_2024/7vhj_31996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/03_2024/7vhj_31996.pdb" } resolution = 4.2 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 16167 2.51 5 N 4220 2.21 5 O 4852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 768": "OD1" <-> "OD2" Residue "B PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 972": "OD1" <-> "OD2" Residue "B GLU 983": "OE1" <-> "OE2" Residue "B ASP 987": "OD1" <-> "OD2" Residue "B ASP 1034": "OD1" <-> "OD2" Residue "B TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ASP 789": "OD1" <-> "OD2" Residue "A ASP 929": "OD1" <-> "OD2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 987": "OD1" <-> "OD2" Residue "A GLU 1085": "OE1" <-> "OE2" Residue "A PHE 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 738": "OD1" <-> "OD2" Residue "C PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 860": "OD1" <-> "OD2" Residue "C PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1139": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25353 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8485 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8457 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8411 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 13.14, per 1000 atoms: 0.52 Number of scatterers: 25353 At special positions: 0 Unit cell: (154.96, 160.16, 192.4, 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 4852 8.00 N 4220 7.00 C 16167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 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=2.04 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 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " 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 Time building additional restraints: 10.09 Conformation dependent library (CDL) restraints added in 4.6 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 48 sheets defined 22.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.138A 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 730 through 736 removed outlier: 3.813A pdb=" N TYR B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 748 removed outlier: 3.760A pdb=" N ASN B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.740A pdb=" N ASN B 757 " --> pdb=" O CYS B 753 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 removed outlier: 3.506A pdb=" N LEU B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 removed outlier: 3.842A pdb=" N LYS B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 843 through 847' Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.816A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 4.289A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 958 Processing helix chain 'B' and resid 959 through 961 No H-bonds generated for 'chain 'B' and resid 959 through 961' Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.983A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 4.273A pdb=" N GLU B1137 " --> pdb=" O PRO B1133 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.917A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.006A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.638A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.259A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 751 through 775 removed outlier: 3.898A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 removed outlier: 4.089A pdb=" N LEU A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.648A pdb=" N PHE A 848 " --> pdb=" O CYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 877 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.184A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 removed outlier: 3.958A pdb=" N THR A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 958 removed outlier: 4.145A pdb=" N GLN A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 961 No H-bonds generated for 'chain 'A' and resid 959 through 961' Processing helix chain 'A' and resid 969 through 977 removed outlier: 3.868A pdb=" N SER A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 976 " --> pdb=" O ASP A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 3.613A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.717A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.613A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 739 through 750 removed outlier: 3.643A pdb=" N GLY C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 776 Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.956A pdb=" N ASN C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 877 Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 905 through 934 removed outlier: 4.309A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS C 914 " --> pdb=" O TYR C 910 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 915 " --> pdb=" O GLU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.063A pdb=" N GLN C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 977 removed outlier: 3.529A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 976 " --> pdb=" O ASP C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.704A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1111 No H-bonds generated for 'chain 'C' and resid 1109 through 1111' Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.942A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 55 removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.759A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.477A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 317 removed outlier: 5.320A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.478A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.575A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.741A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN B 658 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 704 through 708 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.611A pdb=" N MET B1043 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 716 through 720 Processing sheet with id=AB4, first strand: chain 'B' and resid 781 through 783 removed outlier: 5.791A pdb=" N ILE B 781 " --> pdb=" O ASN A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 4.017A pdb=" N CYS B1075 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.543A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.735A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.590A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.671A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 142 through 145 removed outlier: 5.823A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.418A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.713A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.771A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AC8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'A' and resid 551 through 553 removed outlier: 5.623A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.715A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 704 through 720 removed outlier: 3.525A pdb=" N ILE A 707 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1066 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A1064 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 711 " --> pdb=" O PRO A1062 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 713 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A1060 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 715 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1058 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 717 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1056 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 719 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1054 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET A1043 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 704 through 720 removed outlier: 3.525A pdb=" N ILE A 707 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1066 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A1064 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 711 " --> pdb=" O PRO A1062 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 713 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A1060 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 715 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1058 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 717 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1056 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 719 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1054 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A1088 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 727 through 729 removed outlier: 3.828A pdb=" N SER A 728 " --> pdb=" O THR A 852 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1080 through 1081 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.078A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.560A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.640A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.768A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.888A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE7, first strand: chain 'C' and resid 655 through 656 removed outlier: 8.040A pdb=" N VAL C 656 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA C 687 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 704 through 713 removed outlier: 6.919A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 704 through 713 removed outlier: 6.919A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY C1052 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER C1048 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C1054 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C1056 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER C1044 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C1040 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AF2, first strand: chain 'C' and resid 1082 through 1083 Processing sheet with id=AF3, first strand: chain 'C' and resid 1087 through 1089 868 hydrogen bonds defined for protein. 2403 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: 10.55 Time building geometry restraints manager: 10.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8217 1.34 - 1.46: 6265 1.46 - 1.58: 11324 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25950 Sorted by residual: bond pdb=" C ALA C1071 " pdb=" N PRO C1072 " ideal model delta sigma weight residual 1.337 1.323 0.014 9.80e-03 1.04e+04 2.02e+00 bond pdb=" C THR A 588 " pdb=" O THR A 588 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.86e+00 bond pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" C ASP C1132 " pdb=" N PRO C1133 " ideal model delta sigma weight residual 1.336 1.323 0.013 9.80e-03 1.04e+04 1.70e+00 bond pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.56e+00 ... (remaining 25945 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.46: 722 106.46 - 113.36: 14101 113.36 - 120.26: 9008 120.26 - 127.16: 11278 127.16 - 134.05: 237 Bond angle restraints: 35346 Sorted by residual: angle pdb=" C ILE A 587 " pdb=" N THR A 588 " pdb=" CA THR A 588 " ideal model delta sigma weight residual 122.64 118.86 3.78 1.25e+00 6.40e-01 9.15e+00 angle pdb=" N GLN A 173 " pdb=" CA GLN A 173 " pdb=" C GLN A 173 " ideal model delta sigma weight residual 108.97 114.12 -5.15 1.82e+00 3.02e-01 7.99e+00 angle pdb=" N PRO C 979 " pdb=" CA PRO C 979 " pdb=" C PRO C 979 " ideal model delta sigma weight residual 110.70 113.91 -3.21 1.22e+00 6.72e-01 6.91e+00 angle pdb=" C LYS C 847 " pdb=" N PHE C 848 " pdb=" CA PHE C 848 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.90e+00 angle pdb=" CA TRP B 64 " pdb=" CB TRP B 64 " pdb=" CG TRP B 64 " ideal model delta sigma weight residual 113.60 118.49 -4.89 1.90e+00 2.77e-01 6.62e+00 ... (remaining 35341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 14004 17.59 - 35.18: 1220 35.18 - 52.77: 163 52.77 - 70.35: 35 70.35 - 87.94: 20 Dihedral angle restraints: 15442 sinusoidal: 5961 harmonic: 9481 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.29 -87.29 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -6.80 -79.20 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.34 -77.66 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 15439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2871 0.042 - 0.084: 838 0.084 - 0.126: 279 0.126 - 0.168: 18 0.168 - 0.210: 2 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE C 101 " pdb=" CA ILE C 101 " pdb=" CG1 ILE C 101 " pdb=" CG2 ILE C 101 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 4005 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO C 561 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 174 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 585 2.67 - 3.23: 26054 3.23 - 3.78: 39097 3.78 - 4.34: 52634 4.34 - 4.90: 84240 Nonbonded interactions: 202610 Sorted by model distance: nonbonded pdb=" O LEU A 959 " pdb=" OG SER A 968 " model vdw 2.109 2.440 nonbonded pdb=" OH TYR C 749 " pdb=" OD1 ASP C 987 " model vdw 2.120 2.440 nonbonded pdb=" OG1 THR B 376 " pdb=" O ALA B 435 " model vdw 2.125 2.440 nonbonded pdb=" O VAL B1033 " pdb=" OG SER C1023 " model vdw 2.154 2.440 nonbonded pdb=" NH1 ARG B 898 " pdb=" O LEU B1042 " model vdw 2.155 2.520 ... (remaining 202605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 465 or (resid 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 467 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 553 or (resid 554 and (name N or name CA or name C or name O or nam \ e CB )) or resid 555 through 582 or (resid 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 621 or resid 640 through 645 or (re \ sid 646 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 820 or resid 845 through 1140)) selection = (chain 'B' and (resid 27 through 416 or (resid 417 and (name N or name CA or nam \ e C or name O or name CB )) or resid 418 through 423 or (resid 424 and (name N o \ r name CA or name C or name O or name CB )) or resid 425 through 453 or (resid 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 465 or (resid 466 and (name N or name CA or name C or name O or \ name CB )) or resid 467 through 621 or resid 640 through 645 or (resid 646 thro \ ugh 647 and (name N or name CA or name C or name O or name CB )) or resid 648 th \ rough 820 or resid 845 through 1140)) selection = (chain 'C' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 416 or (resid 417 and (name N o \ r name CA or name C or name O or name CB )) or resid 418 through 423 or (resid 4 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 425 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or r \ esid 455 through 456 or (resid 457 and (name N or name CA or name C or name O or \ name CB )) or resid 458 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 582 \ or (resid 583 and (name N or name CA or name C or name O or name CB )) or resid \ 584 through 621 or resid 640 through 1099 or (resid 1100 and (name N or name CA \ or name C or name O or name CB )) or resid 1101 through 1140)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.990 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 66.330 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.004 0.047 25950 Z= 0.260 Angle : 0.646 8.118 35346 Z= 0.359 Chirality : 0.044 0.210 4008 Planarity : 0.004 0.043 4596 Dihedral : 13.111 87.943 9235 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % 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: -3.85 (0.12), residues: 3239 helix: -1.73 (0.17), residues: 667 sheet: -2.15 (0.19), residues: 634 loop : -3.15 (0.12), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 633 HIS 0.011 0.001 HIS B1041 PHE 0.025 0.002 PHE C 899 TYR 0.019 0.002 TYR B 351 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.6300 (p0) cc_final: 0.5142 (m-40) REVERT: B 135 PHE cc_start: 0.7154 (m-10) cc_final: 0.6279 (m-80) REVERT: B 153 MET cc_start: 0.7837 (mtt) cc_final: 0.6955 (tpp) REVERT: B 374 PHE cc_start: 0.6647 (m-10) cc_final: 0.6368 (m-10) REVERT: B 392 PHE cc_start: 0.3311 (p90) cc_final: 0.3061 (p90) REVERT: B 408 ARG cc_start: 0.8176 (ptt90) cc_final: 0.7956 (ptt-90) REVERT: B 862 MET cc_start: 0.8306 (ptp) cc_final: 0.7832 (ptp) REVERT: B 958 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8400 (tt0) REVERT: B 986 ILE cc_start: 0.9296 (mm) cc_final: 0.9009 (mt) REVERT: A 30 ASN cc_start: 0.7892 (t0) cc_final: 0.7499 (m110) REVERT: A 190 ARG cc_start: 0.5731 (mtt180) cc_final: 0.5524 (mtt180) REVERT: A 195 LYS cc_start: 0.8524 (pttt) cc_final: 0.8278 (pttt) REVERT: A 449 TYR cc_start: 0.5651 (m-80) cc_final: 0.5070 (m-10) REVERT: A 516 GLU cc_start: 0.7436 (pm20) cc_final: 0.6680 (pm20) REVERT: A 569 ILE cc_start: 0.8104 (tt) cc_final: 0.7656 (tp) REVERT: A 733 MET cc_start: 0.8651 (tpp) cc_final: 0.8195 (tpt) REVERT: A 767 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8431 (mt0) REVERT: A 881 PHE cc_start: 0.8160 (p90) cc_final: 0.7884 (p90) REVERT: C 129 LYS cc_start: 0.8656 (pttp) cc_final: 0.8377 (pttp) REVERT: C 141 LEU cc_start: 0.8069 (tp) cc_final: 0.7848 (tp) REVERT: C 402 ILE cc_start: 0.8729 (mm) cc_final: 0.8521 (mm) REVERT: C 995 GLN cc_start: 0.8033 (tt0) cc_final: 0.7821 (tp40) outliers start: 2 outliers final: 1 residues processed: 344 average time/residue: 0.3801 time to fit residues: 202.9222 Evaluate side-chains 179 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 253 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 7.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 245 HIS B 271 GLN B 474 GLN B 532 ASN B 744 ASN B 865 GLN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN B 946 ASN B 962 ASN B 998 GLN ** B1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 GLN A 66 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 282 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 564 GLN A 675 GLN A 849 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 188 ASN C 314 GLN C 370 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 544 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS C1064 GLN C1076 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25950 Z= 0.261 Angle : 0.613 8.550 35346 Z= 0.324 Chirality : 0.044 0.166 4008 Planarity : 0.004 0.045 4596 Dihedral : 5.326 24.230 3493 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.07 % Allowed : 5.84 % Favored : 94.09 % 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: -2.88 (0.13), residues: 3239 helix: -0.35 (0.19), residues: 678 sheet: -1.71 (0.19), residues: 629 loop : -2.70 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.008 0.001 HIS C 66 PHE 0.020 0.002 PHE C 157 TYR 0.020 0.002 TYR B 266 ARG 0.005 0.001 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 281 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7772 (mtt) cc_final: 0.6717 (tpp) REVERT: B 266 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.6023 (m-10) REVERT: B 408 ARG cc_start: 0.8094 (ptt90) cc_final: 0.7864 (ptt-90) REVERT: B 986 ILE cc_start: 0.9353 (mm) cc_final: 0.9053 (mt) REVERT: A 30 ASN cc_start: 0.7978 (t0) cc_final: 0.7615 (m110) REVERT: A 195 LYS cc_start: 0.8536 (pttt) cc_final: 0.7880 (pttm) REVERT: A 449 TYR cc_start: 0.5780 (m-80) cc_final: 0.5014 (m-10) REVERT: A 516 GLU cc_start: 0.7234 (pm20) cc_final: 0.6385 (pm20) REVERT: A 733 MET cc_start: 0.8561 (tpp) cc_final: 0.8270 (tpt) REVERT: A 807 LYS cc_start: 0.7855 (mmtt) cc_final: 0.6862 (mmmt) REVERT: C 129 LYS cc_start: 0.8647 (pttp) cc_final: 0.8408 (pttp) REVERT: C 402 ILE cc_start: 0.8687 (mm) cc_final: 0.8426 (mm) REVERT: C 514 SER cc_start: 0.8344 (t) cc_final: 0.8077 (m) REVERT: C 766 GLU cc_start: 0.8233 (tp30) cc_final: 0.7997 (tp30) outliers start: 2 outliers final: 0 residues processed: 283 average time/residue: 0.3414 time to fit residues: 157.6580 Evaluate side-chains 169 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 244 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 318 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 236 optimal weight: 0.2980 overall best weight: 2.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN ** B1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN C 998 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25950 Z= 0.250 Angle : 0.605 8.463 35346 Z= 0.319 Chirality : 0.044 0.171 4008 Planarity : 0.004 0.044 4596 Dihedral : 5.235 24.957 3493 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.33 % 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: -2.45 (0.14), residues: 3239 helix: 0.20 (0.20), residues: 675 sheet: -1.46 (0.20), residues: 632 loop : -2.49 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.012 0.002 HIS C 66 PHE 0.033 0.002 PHE B 816 TYR 0.016 0.002 TYR A 453 ARG 0.009 0.000 ARG A 988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7229 (mtt) cc_final: 0.6778 (tpp) REVERT: B 374 PHE cc_start: 0.6637 (m-10) cc_final: 0.6410 (m-10) REVERT: B 408 ARG cc_start: 0.8113 (ptt90) cc_final: 0.7876 (ptt-90) REVERT: B 425 LEU cc_start: 0.6417 (mt) cc_final: 0.5761 (mp) REVERT: B 767 GLN cc_start: 0.9281 (mm-40) cc_final: 0.9039 (mm-40) REVERT: B 986 ILE cc_start: 0.9379 (mm) cc_final: 0.9042 (mt) REVERT: A 30 ASN cc_start: 0.7853 (t0) cc_final: 0.7521 (m110) REVERT: A 237 ARG cc_start: 0.8296 (mtt180) cc_final: 0.8072 (mtp85) REVERT: A 449 TYR cc_start: 0.5735 (m-80) cc_final: 0.4992 (m-10) REVERT: A 516 GLU cc_start: 0.7138 (pm20) cc_final: 0.6695 (pm20) REVERT: A 733 MET cc_start: 0.8420 (tpp) cc_final: 0.8142 (tpt) REVERT: A 807 LYS cc_start: 0.7899 (mmtt) cc_final: 0.6892 (mmmt) REVERT: C 129 LYS cc_start: 0.8689 (pttp) cc_final: 0.8446 (pttp) REVERT: C 153 MET cc_start: 0.7038 (mmm) cc_final: 0.6832 (mmm) REVERT: C 402 ILE cc_start: 0.8741 (mm) cc_final: 0.8443 (mm) REVERT: C 571 ASP cc_start: 0.7243 (t70) cc_final: 0.6971 (t0) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.3606 time to fit residues: 156.2177 Evaluate side-chains 162 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 313 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 280 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 998 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 744 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25950 Z= 0.339 Angle : 0.653 10.031 35346 Z= 0.345 Chirality : 0.045 0.181 4008 Planarity : 0.004 0.071 4596 Dihedral : 5.440 24.251 3493 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: -2.38 (0.14), residues: 3239 helix: 0.26 (0.20), residues: 664 sheet: -1.35 (0.20), residues: 636 loop : -2.46 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 104 HIS 0.011 0.002 HIS A 66 PHE 0.022 0.002 PHE C 157 TYR 0.019 0.002 TYR C 749 ARG 0.010 0.001 ARG A 988 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7342 (mtt) cc_final: 0.6957 (tpp) REVERT: B 392 PHE cc_start: 0.3381 (p90) cc_final: 0.2864 (p90) REVERT: B 408 ARG cc_start: 0.8094 (ptt90) cc_final: 0.7834 (ptt-90) REVERT: B 986 ILE cc_start: 0.9351 (mm) cc_final: 0.9063 (mt) REVERT: A 30 ASN cc_start: 0.7852 (t0) cc_final: 0.7463 (m110) REVERT: A 195 LYS cc_start: 0.8379 (pttt) cc_final: 0.8031 (pttm) REVERT: A 449 TYR cc_start: 0.5855 (m-80) cc_final: 0.5101 (m-10) REVERT: A 516 GLU cc_start: 0.7493 (pm20) cc_final: 0.7134 (pm20) REVERT: A 807 LYS cc_start: 0.7875 (mmtt) cc_final: 0.6876 (mmmt) REVERT: C 129 LYS cc_start: 0.8707 (pttp) cc_final: 0.8474 (pttp) REVERT: C 153 MET cc_start: 0.7318 (mmm) cc_final: 0.7091 (mmm) REVERT: C 402 ILE cc_start: 0.8741 (mm) cc_final: 0.8479 (mm) REVERT: C 571 ASP cc_start: 0.7418 (t70) cc_final: 0.7103 (t0) REVERT: C 894 GLN cc_start: 0.8582 (tt0) cc_final: 0.8174 (tp40) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3332 time to fit residues: 139.7016 Evaluate side-chains 157 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 159 optimal weight: 0.0270 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25950 Z= 0.242 Angle : 0.589 8.616 35346 Z= 0.310 Chirality : 0.044 0.207 4008 Planarity : 0.004 0.071 4596 Dihedral : 5.183 24.308 3493 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -2.13 (0.14), residues: 3239 helix: 0.58 (0.20), residues: 665 sheet: -1.26 (0.20), residues: 659 loop : -2.31 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.009 0.001 HIS A 66 PHE 0.028 0.001 PHE B 374 TYR 0.018 0.001 TYR C 897 ARG 0.008 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7541 (mtt) cc_final: 0.7020 (tpp) REVERT: B 228 ASP cc_start: 0.7375 (t0) cc_final: 0.7112 (t0) REVERT: B 392 PHE cc_start: 0.3321 (p90) cc_final: 0.2703 (p90) REVERT: B 408 ARG cc_start: 0.8096 (ptt90) cc_final: 0.7837 (ptt-90) REVERT: B 425 LEU cc_start: 0.6135 (mt) cc_final: 0.5136 (mp) REVERT: B 986 ILE cc_start: 0.9368 (mm) cc_final: 0.9027 (mt) REVERT: A 30 ASN cc_start: 0.7687 (t0) cc_final: 0.7468 (m110) REVERT: A 195 LYS cc_start: 0.8348 (pttt) cc_final: 0.7239 (pttt) REVERT: A 449 TYR cc_start: 0.5947 (m-80) cc_final: 0.5158 (m-10) REVERT: A 516 GLU cc_start: 0.7450 (pm20) cc_final: 0.7237 (pm20) REVERT: A 807 LYS cc_start: 0.7842 (mmtt) cc_final: 0.6854 (mmmt) REVERT: A 1022 MET cc_start: 0.8733 (tpp) cc_final: 0.8379 (tpp) REVERT: C 129 LYS cc_start: 0.8712 (pttp) cc_final: 0.8493 (pttp) REVERT: C 153 MET cc_start: 0.7346 (mmm) cc_final: 0.7122 (mmm) REVERT: C 402 ILE cc_start: 0.8641 (mm) cc_final: 0.8412 (mm) REVERT: C 571 ASP cc_start: 0.7367 (t70) cc_final: 0.7064 (t0) REVERT: C 894 GLN cc_start: 0.8390 (tt0) cc_final: 0.8002 (tp40) REVERT: C 1043 MET cc_start: 0.8365 (ptp) cc_final: 0.7796 (ptp) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3309 time to fit residues: 142.4437 Evaluate side-chains 155 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 313 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 26 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25950 Z= 0.197 Angle : 0.573 8.997 35346 Z= 0.298 Chirality : 0.043 0.199 4008 Planarity : 0.004 0.078 4596 Dihedral : 4.996 26.697 3493 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -1.90 (0.14), residues: 3239 helix: 0.84 (0.21), residues: 662 sheet: -1.06 (0.20), residues: 645 loop : -2.21 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.009 0.001 HIS A 66 PHE 0.026 0.001 PHE C 157 TYR 0.018 0.001 TYR B 897 ARG 0.004 0.000 ARG A 988 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 4.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7583 (mtt) cc_final: 0.6966 (tpp) REVERT: B 228 ASP cc_start: 0.7323 (t0) cc_final: 0.6994 (t0) REVERT: B 281 GLU cc_start: 0.6848 (pm20) cc_final: 0.6635 (pm20) REVERT: B 408 ARG cc_start: 0.8049 (ptt90) cc_final: 0.7799 (ptt-90) REVERT: B 425 LEU cc_start: 0.6342 (mt) cc_final: 0.6080 (tp) REVERT: B 582 LEU cc_start: 0.8177 (mt) cc_final: 0.7766 (pp) REVERT: B 986 ILE cc_start: 0.9304 (mm) cc_final: 0.8943 (mt) REVERT: A 195 LYS cc_start: 0.8385 (pttt) cc_final: 0.7873 (ptpp) REVERT: A 449 TYR cc_start: 0.5893 (m-80) cc_final: 0.4995 (m-10) REVERT: A 807 LYS cc_start: 0.7779 (mmtt) cc_final: 0.6780 (mmmt) REVERT: A 1022 MET cc_start: 0.8706 (tpp) cc_final: 0.8412 (tpp) REVERT: C 129 LYS cc_start: 0.8677 (pttp) cc_final: 0.8393 (pttp) REVERT: C 153 MET cc_start: 0.7310 (mmm) cc_final: 0.7086 (mmm) REVERT: C 402 ILE cc_start: 0.8713 (mm) cc_final: 0.8345 (mm) REVERT: C 571 ASP cc_start: 0.7400 (t70) cc_final: 0.7147 (t0) REVERT: C 1043 MET cc_start: 0.8430 (ptp) cc_final: 0.8222 (ptp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3102 time to fit residues: 140.9260 Evaluate side-chains 160 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.0870 chunk 35 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 228 optimal weight: 0.0040 chunk 177 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 175 optimal weight: 0.1980 chunk 312 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.8372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 487 ASN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN C 536 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25950 Z= 0.167 Angle : 0.556 9.248 35346 Z= 0.290 Chirality : 0.043 0.170 4008 Planarity : 0.004 0.071 4596 Dihedral : 4.777 27.934 3493 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -1.65 (0.15), residues: 3239 helix: 1.16 (0.21), residues: 661 sheet: -0.93 (0.20), residues: 652 loop : -2.08 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 633 HIS 0.014 0.001 HIS C 66 PHE 0.033 0.001 PHE A 275 TYR 0.016 0.001 TYR B 866 ARG 0.004 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7560 (mtt) cc_final: 0.6875 (tpp) REVERT: B 228 ASP cc_start: 0.7353 (t0) cc_final: 0.7120 (t0) REVERT: B 374 PHE cc_start: 0.6669 (m-10) cc_final: 0.6205 (m-80) REVERT: B 408 ARG cc_start: 0.8074 (ptt90) cc_final: 0.7826 (ptt-90) REVERT: B 582 LEU cc_start: 0.8079 (mt) cc_final: 0.7774 (pp) REVERT: B 723 SER cc_start: 0.8978 (t) cc_final: 0.8770 (t) REVERT: B 986 ILE cc_start: 0.9260 (mm) cc_final: 0.8838 (mt) REVERT: A 195 LYS cc_start: 0.8443 (pttt) cc_final: 0.7832 (ptpp) REVERT: A 692 LEU cc_start: 0.8834 (mp) cc_final: 0.8597 (mp) REVERT: A 724 MET cc_start: 0.8526 (ptp) cc_final: 0.8248 (ptm) REVERT: A 807 LYS cc_start: 0.7664 (mmtt) cc_final: 0.6690 (mmmt) REVERT: A 895 MET cc_start: 0.7953 (mmp) cc_final: 0.7741 (mmp) REVERT: A 1022 MET cc_start: 0.8697 (tpp) cc_final: 0.8380 (tpp) REVERT: C 129 LYS cc_start: 0.8648 (pttp) cc_final: 0.8366 (pttp) REVERT: C 153 MET cc_start: 0.7265 (mmm) cc_final: 0.7026 (mmm) REVERT: C 402 ILE cc_start: 0.8662 (mm) cc_final: 0.8311 (mm) REVERT: C 571 ASP cc_start: 0.7297 (t70) cc_final: 0.7050 (t0) REVERT: C 664 ILE cc_start: 0.9035 (mm) cc_final: 0.8794 (mm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.3219 time to fit residues: 146.1581 Evaluate side-chains 170 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.0270 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 245 optimal weight: 0.0060 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN C 317 ASN C 519 HIS C 564 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25950 Z= 0.165 Angle : 0.555 8.794 35346 Z= 0.288 Chirality : 0.043 0.220 4008 Planarity : 0.004 0.064 4596 Dihedral : 4.620 25.741 3493 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.04 % Allowed : 0.57 % Favored : 99.40 % 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: -1.52 (0.15), residues: 3239 helix: 1.30 (0.21), residues: 661 sheet: -0.78 (0.20), residues: 640 loop : -2.03 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 633 HIS 0.012 0.001 HIS C 66 PHE 0.028 0.001 PHE C 157 TYR 0.015 0.001 TYR C 265 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7546 (mtt) cc_final: 0.6827 (tpp) REVERT: B 281 GLU cc_start: 0.6774 (pm20) cc_final: 0.6506 (pm20) REVERT: B 408 ARG cc_start: 0.8081 (ptt90) cc_final: 0.7865 (ptt-90) REVERT: B 582 LEU cc_start: 0.8041 (mt) cc_final: 0.7783 (pp) REVERT: A 176 LEU cc_start: 0.8313 (mt) cc_final: 0.8101 (mt) REVERT: A 177 MET cc_start: 0.5868 (mmm) cc_final: 0.5562 (tpp) REVERT: A 195 LYS cc_start: 0.8551 (pttt) cc_final: 0.8190 (pttm) REVERT: A 692 LEU cc_start: 0.8718 (mp) cc_final: 0.8425 (mp) REVERT: A 807 LYS cc_start: 0.7638 (mmtt) cc_final: 0.6761 (mmmt) REVERT: C 129 LYS cc_start: 0.8631 (pttp) cc_final: 0.8390 (pttp) REVERT: C 153 MET cc_start: 0.7221 (mmm) cc_final: 0.7009 (mmm) REVERT: C 402 ILE cc_start: 0.8583 (mm) cc_final: 0.8298 (mm) REVERT: C 571 ASP cc_start: 0.7315 (t70) cc_final: 0.7083 (t0) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.3214 time to fit residues: 145.0129 Evaluate side-chains 171 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.9990 chunk 299 optimal weight: 0.2980 chunk 272 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 175 optimal weight: 0.0070 chunk 126 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 0.0570 chunk 275 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 894 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN C 115 GLN C 563 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25950 Z= 0.157 Angle : 0.542 8.494 35346 Z= 0.282 Chirality : 0.042 0.172 4008 Planarity : 0.004 0.063 4596 Dihedral : 4.530 24.811 3493 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.04 % Allowed : 0.57 % Favored : 99.40 % 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: -1.39 (0.15), residues: 3239 helix: 1.35 (0.21), residues: 663 sheet: -0.65 (0.21), residues: 641 loop : -1.94 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.021 0.001 HIS B1041 PHE 0.033 0.001 PHE C 392 TYR 0.019 0.001 TYR C 897 ARG 0.005 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7565 (mtt) cc_final: 0.6834 (tpp) REVERT: B 281 GLU cc_start: 0.6717 (pm20) cc_final: 0.6463 (pm20) REVERT: B 374 PHE cc_start: 0.6639 (m-10) cc_final: 0.6177 (m-80) REVERT: B 408 ARG cc_start: 0.8109 (ptt90) cc_final: 0.7904 (ptt-90) REVERT: B 911 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 912 ASN cc_start: 0.7247 (m-40) cc_final: 0.6493 (m-40) REVERT: B 986 ILE cc_start: 0.9256 (mm) cc_final: 0.8666 (mt) REVERT: A 176 LEU cc_start: 0.8245 (mt) cc_final: 0.7997 (mt) REVERT: A 177 MET cc_start: 0.5641 (mmm) cc_final: 0.5321 (mmm) REVERT: A 195 LYS cc_start: 0.8505 (pttt) cc_final: 0.8100 (pttm) REVERT: A 449 TYR cc_start: 0.5722 (m-80) cc_final: 0.5016 (m-10) REVERT: A 807 LYS cc_start: 0.7560 (mmtt) cc_final: 0.6771 (mmmt) REVERT: C 129 LYS cc_start: 0.8645 (pttp) cc_final: 0.8398 (pttp) REVERT: C 153 MET cc_start: 0.7368 (mmm) cc_final: 0.7106 (mmm) REVERT: C 402 ILE cc_start: 0.8576 (mm) cc_final: 0.8276 (tt) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.3250 time to fit residues: 150.2701 Evaluate side-chains 183 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN B 894 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25950 Z= 0.209 Angle : 0.571 8.456 35346 Z= 0.298 Chirality : 0.043 0.262 4008 Planarity : 0.004 0.065 4596 Dihedral : 4.622 24.947 3493 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % 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: -1.41 (0.15), residues: 3239 helix: 1.30 (0.21), residues: 668 sheet: -0.77 (0.21), residues: 648 loop : -1.91 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.011 0.001 HIS A 66 PHE 0.030 0.001 PHE C 157 TYR 0.018 0.001 TYR B 866 ARG 0.007 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7591 (mtt) cc_final: 0.6908 (tpp) REVERT: B 237 ARG cc_start: 0.7977 (tpm170) cc_final: 0.7776 (tpp-160) REVERT: B 281 GLU cc_start: 0.6876 (pm20) cc_final: 0.6607 (pm20) REVERT: B 374 PHE cc_start: 0.6575 (m-10) cc_final: 0.6137 (m-80) REVERT: B 582 LEU cc_start: 0.7996 (mt) cc_final: 0.7748 (pp) REVERT: B 893 MET cc_start: 0.8137 (mmt) cc_final: 0.7811 (mmm) REVERT: A 176 LEU cc_start: 0.8208 (mt) cc_final: 0.7958 (mt) REVERT: A 177 MET cc_start: 0.5631 (mmm) cc_final: 0.5285 (mmm) REVERT: A 195 LYS cc_start: 0.8526 (pttt) cc_final: 0.8140 (pttm) REVERT: A 724 MET cc_start: 0.8520 (ptm) cc_final: 0.8208 (ptm) REVERT: A 807 LYS cc_start: 0.7544 (mmtt) cc_final: 0.6728 (mmmt) REVERT: C 129 LYS cc_start: 0.8645 (pttp) cc_final: 0.8377 (pttp) REVERT: C 153 MET cc_start: 0.7356 (mmm) cc_final: 0.7096 (mmm) REVERT: C 317 ASN cc_start: 0.7827 (t0) cc_final: 0.7606 (p0) REVERT: C 402 ILE cc_start: 0.8581 (mm) cc_final: 0.8305 (mm) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.3199 time to fit residues: 139.7169 Evaluate side-chains 168 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN C 370 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 GLN ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.077008 restraints weight = 86924.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076779 restraints weight = 71422.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077091 restraints weight = 57557.421| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25950 Z= 0.323 Angle : 0.642 8.617 35346 Z= 0.335 Chirality : 0.044 0.180 4008 Planarity : 0.004 0.072 4596 Dihedral : 5.002 23.466 3493 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -1.58 (0.15), residues: 3239 helix: 0.95 (0.21), residues: 680 sheet: -0.90 (0.20), residues: 692 loop : -1.96 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.012 0.002 HIS A 66 PHE 0.029 0.002 PHE C 157 TYR 0.019 0.002 TYR B 897 ARG 0.006 0.001 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4512.96 seconds wall clock time: 83 minutes 18.95 seconds (4998.95 seconds total)