Starting phenix.real_space_refine on Wed Dec 13 11:45:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/12_2023/8h14_34424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/12_2023/8h14_34424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/12_2023/8h14_34424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/12_2023/8h14_34424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/12_2023/8h14_34424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/12_2023/8h14_34424_updated.pdb" } resolution = 3.39 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= 0.014 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 141 5.16 5 C 15801 2.51 5 N 4029 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 790": "OD1" <-> "OD2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A TYR 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1121": "OD1" <-> "OD2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 684": "OD1" <-> "OD2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 790": "OD1" <-> "OD2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "B TYR 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1074": "OE1" <-> "OE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1121": "OD1" <-> "OD2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 684": "OD1" <-> "OD2" Residue "C TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C TYR 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1074": "OE1" <-> "OE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1121": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 24750 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8034 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 49, 'TRANS': 979} Chain breaks: 6 Chain: "B" Number of atoms: 8034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8034 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 49, 'TRANS': 979} Chain breaks: 6 Chain: "C" Number of atoms: 8034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8034 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 49, 'TRANS': 979} Chain breaks: 6 Chain: "A" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 12.64, per 1000 atoms: 0.51 Number of scatterers: 24750 At special positions: 0 Unit cell: (121.5, 126.9, 174.15, 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 141 16.00 O 4779 8.00 N 4029 7.00 C 15801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 414 " - pdb=" SG CYS C 969 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A 969 " - pdb=" SG CYS B 414 " distance=2.07 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.07 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B 969 " - pdb=" SG CYS C 414 " distance=1.99 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.07 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A1080 " " NAG A1303 " - " ASN A 109 " " NAG A1304 " - " ASN A 119 " " NAG A1305 " - " ASN A 158 " " NAG A1306 " - " ASN A 227 " " NAG A1307 " - " ASN A 269 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 330 " " NAG A1310 " - " ASN A 357 " " NAG A1311 " - " ASN A 602 " " NAG A1312 " - " ASN A 699 " " NAG A1313 " - " ASN A 783 " " NAG A1314 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 227 " " NAG B1307 " - " ASN B 269 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 330 " " NAG B1310 " - " ASN B 357 " " NAG B1311 " - " ASN B 602 " " NAG B1312 " - " ASN B 699 " " NAG B1313 " - " ASN B 783 " " NAG B1314 " - " ASN B1116 " " NAG C1302 " - " ASN C 65 " " NAG C1303 " - " ASN C1080 " " NAG C1304 " - " ASN C 109 " " NAG C1305 " - " ASN C 119 " " NAG C1306 " - " ASN C 158 " " NAG C1307 " - " ASN C 227 " " NAG C1308 " - " ASN C 269 " " NAG C1309 " - " ASN C 318 " " NAG C1310 " - " ASN C 330 " " NAG C1311 " - " ASN C 357 " " NAG C1312 " - " ASN C 602 " " NAG C1313 " - " ASN C 699 " " NAG C1314 " - " ASN C 783 " " NAG C1315 " - " ASN C1116 " Time building additional restraints: 9.66 Conformation dependent library (CDL) restraints added in 4.4 seconds 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 39 sheets defined 23.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.583A pdb=" N LEU A 355 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 356' Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.561A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 729 through 764 removed outlier: 4.817A pdb=" N GLN A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE A 741 " --> pdb=" O GLN A 737 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 865 Processing helix chain 'A' and resid 869 through 872 No H-bonds generated for 'chain 'A' and resid 869 through 872' Processing helix chain 'A' and resid 880 through 891 removed outlier: 3.703A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 902 through 921 Processing helix chain 'A' and resid 928 through 949 removed outlier: 3.753A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 Processing helix chain 'A' and resid 968 through 1014 removed outlier: 4.653A pdb=" N VAL A 973 " --> pdb=" O CYS A 969 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.582A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.560A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'B' and resid 729 through 764 removed outlier: 4.816A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE B 741 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 865 Processing helix chain 'B' and resid 869 through 872 No H-bonds generated for 'chain 'B' and resid 869 through 872' Processing helix chain 'B' and resid 880 through 891 removed outlier: 3.703A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 902 through 921 Processing helix chain 'B' and resid 928 through 949 removed outlier: 3.754A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 968 through 1014 removed outlier: 4.654A pdb=" N VAL B 973 " --> pdb=" O CYS B 969 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.583A pdb=" N LEU C 355 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 356' Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.561A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 426 through 429 No H-bonds generated for 'chain 'C' and resid 426 through 429' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 720 through 724 Processing helix chain 'C' and resid 729 through 764 removed outlier: 4.815A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER C 740 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE C 741 " --> pdb=" O GLN C 737 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 742 " --> pdb=" O TYR C 738 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 865 Processing helix chain 'C' and resid 869 through 872 No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 880 through 891 removed outlier: 3.702A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 902 through 921 Processing helix chain 'C' and resid 928 through 949 removed outlier: 3.754A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 965 Processing helix chain 'C' and resid 968 through 1014 removed outlier: 4.654A pdb=" N VAL C 973 " --> pdb=" O CYS C 969 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.839A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.127A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 164 removed outlier: 5.980A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 298 through 301 Processing sheet with id= E, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.181A pdb=" N GLY A 311 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.238A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 439 through 441 Processing sheet with id= H, first strand: chain 'A' and resid 673 through 678 removed outlier: 6.692A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 693 through 697 Processing sheet with id= J, first strand: chain 'A' and resid 699 through 710 removed outlier: 6.342A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.583A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= M, first strand: chain 'A' and resid 1076 through 1079 Processing sheet with id= N, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.839A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.126A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 161 through 164 removed outlier: 5.981A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 298 through 301 Processing sheet with id= R, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.181A pdb=" N GLY B 311 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.239A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 439 through 441 Processing sheet with id= U, first strand: chain 'B' and resid 673 through 678 removed outlier: 6.692A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 693 through 697 Processing sheet with id= W, first strand: chain 'B' and resid 699 through 710 removed outlier: 6.342A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.582A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id= Z, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id= AA, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.839A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.126A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 161 through 164 removed outlier: 5.981A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 298 through 301 Processing sheet with id= AE, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.181A pdb=" N GLY C 311 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.239A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 439 through 441 Processing sheet with id= AH, first strand: chain 'C' and resid 673 through 678 removed outlier: 6.692A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 693 through 697 Processing sheet with id= AJ, first strand: chain 'C' and resid 699 through 710 removed outlier: 6.342A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.582A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 1063 through 1065 Processing sheet with id= AM, first strand: chain 'C' and resid 1076 through 1079 906 hydrogen bonds defined for protein. 2520 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: 10.42 Time building geometry restraints manager: 10.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 7932 1.37 - 1.52: 12342 1.52 - 1.68: 4845 1.68 - 1.83: 180 1.83 - 1.99: 6 Bond restraints: 25305 Sorted by residual: bond pdb=" CB CYS C 419 " pdb=" SG CYS C 419 " ideal model delta sigma weight residual 1.808 1.988 -0.180 3.30e-02 9.18e+02 2.98e+01 bond pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " ideal model delta sigma weight residual 1.808 1.988 -0.180 3.30e-02 9.18e+02 2.98e+01 bond pdb=" CB CYS A 419 " pdb=" SG CYS A 419 " ideal model delta sigma weight residual 1.808 1.988 -0.180 3.30e-02 9.18e+02 2.98e+01 bond pdb=" CB CYS A 366 " pdb=" SG CYS A 366 " ideal model delta sigma weight residual 1.808 1.651 0.157 3.30e-02 9.18e+02 2.26e+01 bond pdb=" CB CYS C 366 " pdb=" SG CYS C 366 " ideal model delta sigma weight residual 1.808 1.651 0.157 3.30e-02 9.18e+02 2.25e+01 ... (remaining 25300 not shown) Histogram of bond angle deviations from ideal: 96.52 - 106.04: 597 106.04 - 115.56: 15579 115.56 - 125.08: 17855 125.08 - 134.60: 346 134.60 - 144.12: 3 Bond angle restraints: 34380 Sorted by residual: angle pdb=" CA CYS C 366 " pdb=" CB CYS C 366 " pdb=" SG CYS C 366 " ideal model delta sigma weight residual 114.40 144.12 -29.72 2.30e+00 1.89e-01 1.67e+02 angle pdb=" CA CYS A 366 " pdb=" CB CYS A 366 " pdb=" SG CYS A 366 " ideal model delta sigma weight residual 114.40 144.11 -29.71 2.30e+00 1.89e-01 1.67e+02 angle pdb=" CA CYS B 366 " pdb=" CB CYS B 366 " pdb=" SG CYS B 366 " ideal model delta sigma weight residual 114.40 144.10 -29.70 2.30e+00 1.89e-01 1.67e+02 angle pdb=" C PHE B 130 " pdb=" CA PHE B 130 " pdb=" CB PHE B 130 " ideal model delta sigma weight residual 109.79 96.52 13.27 2.05e+00 2.38e-01 4.19e+01 angle pdb=" C PHE C 130 " pdb=" CA PHE C 130 " pdb=" CB PHE C 130 " ideal model delta sigma weight residual 109.79 96.52 13.27 2.05e+00 2.38e-01 4.19e+01 ... (remaining 34375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14129 17.77 - 35.55: 1137 35.55 - 53.32: 289 53.32 - 71.10: 51 71.10 - 88.87: 24 Dihedral angle restraints: 15630 sinusoidal: 6642 harmonic: 8988 Sorted by residual: dihedral pdb=" CB CYS A 648 " pdb=" SG CYS A 648 " pdb=" SG CYS A 657 " pdb=" CB CYS A 657 " ideal model delta sinusoidal sigma weight residual -86.00 2.49 -88.49 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS C 648 " pdb=" SG CYS C 648 " pdb=" SG CYS C 657 " pdb=" CB CYS C 657 " ideal model delta sinusoidal sigma weight residual -86.00 2.47 -88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual -86.00 2.46 -88.46 1 1.00e+01 1.00e-02 9.34e+01 ... (remaining 15627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3896 0.136 - 0.272: 85 0.272 - 0.407: 0 0.407 - 0.543: 3 0.543 - 0.679: 6 Chirality restraints: 3990 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B1080 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1080 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C1080 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3987 not shown) Planarity restraints: 4434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 699 " -0.048 2.00e-02 2.50e+03 4.65e-02 2.71e+01 pdb=" CG ASN A 699 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 699 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 699 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG A1312 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 699 " -0.048 2.00e-02 2.50e+03 4.65e-02 2.70e+01 pdb=" CG ASN C 699 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 699 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 699 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG C1313 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 699 " -0.048 2.00e-02 2.50e+03 4.62e-02 2.67e+01 pdb=" CG ASN B 699 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 699 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 699 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG B1312 " -0.048 2.00e-02 2.50e+03 ... (remaining 4431 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1055 2.72 - 3.27: 21779 3.27 - 3.81: 36548 3.81 - 4.36: 46504 4.36 - 4.90: 82678 Nonbonded interactions: 188564 Sorted by model distance: nonbonded pdb=" O THR C 925 " pdb=" OG1 THR C 925 " model vdw 2.177 2.440 nonbonded pdb=" O THR A 925 " pdb=" OG1 THR A 925 " model vdw 2.178 2.440 nonbonded pdb=" O THR B 925 " pdb=" OG1 THR B 925 " model vdw 2.179 2.440 nonbonded pdb=" O ASN C 960 " pdb=" OG SER C 964 " model vdw 2.243 2.440 nonbonded pdb=" O ASN A 960 " pdb=" OG SER A 964 " model vdw 2.244 2.440 ... (remaining 188559 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 31 through 1123 or resid 1302 through 1314)) selection = (chain 'B' and (resid 31 through 1123 or resid 1302 through 1314)) selection = (chain 'C' and (resid 31 through 1123 or resid 1302 through 1314)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.790 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 66.760 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.005 0.180 25305 Z= 0.345 Angle : 0.954 29.719 34380 Z= 0.518 Chirality : 0.063 0.679 3990 Planarity : 0.006 0.057 4392 Dihedral : 13.867 88.870 9717 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.35 % Allowed : 1.46 % Favored : 97.19 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3045 helix: 0.48 (0.19), residues: 666 sheet: 0.80 (0.20), residues: 687 loop : -1.66 (0.12), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 619 HIS 0.006 0.001 HIS B 181 PHE 0.035 0.002 PHE A 130 TYR 0.024 0.002 TYR A 886 ARG 0.014 0.001 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 2.633 Fit side-chains outliers start: 36 outliers final: 13 residues processed: 278 average time/residue: 0.3735 time to fit residues: 162.5772 Evaluate side-chains 189 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3181 time to fit residues: 10.3385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A 939 GLN B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B 931 GLN C 181 HIS C 877 GLN C 939 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25305 Z= 0.173 Angle : 0.520 7.824 34380 Z= 0.274 Chirality : 0.046 0.311 3990 Planarity : 0.004 0.041 4392 Dihedral : 7.257 57.677 4242 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.79 % Allowed : 6.44 % Favored : 92.77 % 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: -0.28 (0.14), residues: 3045 helix: 1.49 (0.21), residues: 666 sheet: 0.81 (0.19), residues: 726 loop : -1.44 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 423 HIS 0.002 0.001 HIS C 181 PHE 0.026 0.001 PHE B 130 TYR 0.017 0.001 TYR C1049 ARG 0.003 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 3.588 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 215 average time/residue: 0.3878 time to fit residues: 132.0536 Evaluate side-chains 182 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2299 time to fit residues: 8.6344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 0.0770 chunk 300 optimal weight: 0.0370 chunk 247 optimal weight: 0.9990 chunk 276 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN B 904 GLN B 917 GLN C 883 GLN C 917 GLN C 939 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 25305 Z= 0.209 Angle : 0.522 10.926 34380 Z= 0.274 Chirality : 0.047 0.293 3990 Planarity : 0.004 0.035 4392 Dihedral : 6.317 55.090 4242 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.97 % Allowed : 8.69 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3045 helix: 1.56 (0.21), residues: 684 sheet: 1.06 (0.19), residues: 726 loop : -1.44 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 423 HIS 0.002 0.000 HIS B1040 PHE 0.016 0.001 PHE B 130 TYR 0.021 0.001 TYR C1049 ARG 0.003 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 2.821 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 199 average time/residue: 0.3543 time to fit residues: 114.4544 Evaluate side-chains 168 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2324 time to fit residues: 8.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 279 optimal weight: 0.0070 chunk 295 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 264 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN C 877 GLN C 939 GLN C 984 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25305 Z= 0.166 Angle : 0.493 14.466 34380 Z= 0.258 Chirality : 0.045 0.288 3990 Planarity : 0.003 0.034 4392 Dihedral : 5.840 53.952 4242 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.97 % Allowed : 9.18 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3045 helix: 1.72 (0.21), residues: 687 sheet: 1.08 (0.19), residues: 711 loop : -1.32 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 423 HIS 0.001 0.000 HIS C 33 PHE 0.012 0.001 PHE A 130 TYR 0.017 0.001 TYR C1049 ARG 0.002 0.000 ARG C 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 200 average time/residue: 0.3763 time to fit residues: 120.6500 Evaluate side-chains 188 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2334 time to fit residues: 12.8025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 917 GLN B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN C 939 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 25305 Z= 0.214 Angle : 0.513 14.002 34380 Z= 0.269 Chirality : 0.046 0.285 3990 Planarity : 0.004 0.033 4392 Dihedral : 5.644 51.056 4242 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.56 % Allowed : 10.71 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3045 helix: 1.81 (0.21), residues: 672 sheet: 0.85 (0.20), residues: 621 loop : -1.30 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 868 HIS 0.002 0.001 HIS A1040 PHE 0.017 0.001 PHE A 130 TYR 0.019 0.001 TYR C1049 ARG 0.003 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 2.821 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 194 average time/residue: 0.3886 time to fit residues: 119.8529 Evaluate side-chains 173 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 2.695 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2937 time to fit residues: 9.6038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 4.9990 chunk 266 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN C 889 ASN C 895 GLN C 939 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25305 Z= 0.260 Angle : 0.538 13.415 34380 Z= 0.282 Chirality : 0.047 0.293 3990 Planarity : 0.004 0.035 4392 Dihedral : 5.700 53.385 4242 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.56 % Allowed : 11.65 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3045 helix: 1.64 (0.21), residues: 687 sheet: 0.79 (0.20), residues: 621 loop : -1.40 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.002 0.001 HIS B1046 PHE 0.018 0.001 PHE A 130 TYR 0.020 0.001 TYR C1049 ARG 0.003 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 187 average time/residue: 0.3772 time to fit residues: 112.7108 Evaluate side-chains 170 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 2.871 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2930 time to fit residues: 9.4789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 6.9990 chunk 33 optimal weight: 0.0570 chunk 168 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 0.2980 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN C 877 GLN C 889 ASN C 895 GLN C 896 ASN C 939 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25305 Z= 0.211 Angle : 0.515 15.302 34380 Z= 0.269 Chirality : 0.046 0.288 3990 Planarity : 0.004 0.035 4392 Dihedral : 5.548 53.365 4242 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.49 % Allowed : 12.02 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3045 helix: 1.69 (0.21), residues: 687 sheet: 0.79 (0.20), residues: 621 loop : -1.36 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 868 HIS 0.002 0.000 HIS B1046 PHE 0.015 0.001 PHE A 130 TYR 0.019 0.001 TYR C1049 ARG 0.002 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 2.801 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 182 average time/residue: 0.3737 time to fit residues: 109.9581 Evaluate side-chains 167 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2314 time to fit residues: 6.5422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 187 optimal weight: 0.4980 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN C 895 GLN C 939 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25305 Z= 0.183 Angle : 0.499 15.064 34380 Z= 0.260 Chirality : 0.045 0.289 3990 Planarity : 0.003 0.034 4392 Dihedral : 5.371 53.291 4242 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.49 % Allowed : 12.32 % Favored : 87.19 % 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: -0.18 (0.15), residues: 3045 helix: 1.74 (0.21), residues: 690 sheet: 0.77 (0.20), residues: 624 loop : -1.31 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 868 HIS 0.002 0.000 HIS B1065 PHE 0.013 0.001 PHE A 130 TYR 0.018 0.001 TYR C1049 ARG 0.002 0.000 ARG C1021 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 2.675 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 183 average time/residue: 0.3763 time to fit residues: 110.8628 Evaluate side-chains 174 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2351 time to fit residues: 8.1689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.7762 > 50: distance: 23 - 29: 9.928 distance: 29 - 30: 8.666 distance: 30 - 31: 5.698 distance: 30 - 33: 5.305 distance: 31 - 32: 12.302 distance: 31 - 40: 6.883 distance: 33 - 34: 11.523 distance: 34 - 35: 3.498 distance: 34 - 36: 9.371 distance: 35 - 37: 16.617 distance: 36 - 38: 20.562 distance: 37 - 39: 7.983 distance: 38 - 39: 8.436 distance: 40 - 41: 7.880 distance: 41 - 42: 6.291 distance: 41 - 44: 15.340 distance: 42 - 43: 7.990 distance: 42 - 46: 10.138 distance: 44 - 45: 20.487 distance: 46 - 47: 6.333 distance: 47 - 48: 7.412 distance: 47 - 50: 14.021 distance: 48 - 49: 5.985 distance: 48 - 55: 7.633 distance: 50 - 51: 12.538 distance: 51 - 52: 8.580 distance: 52 - 53: 12.770 distance: 52 - 54: 20.643 distance: 55 - 56: 11.379 distance: 56 - 57: 4.919 distance: 56 - 59: 5.459 distance: 57 - 58: 9.503 distance: 57 - 63: 9.128 distance: 59 - 60: 8.504 distance: 59 - 61: 12.489 distance: 60 - 62: 21.060 distance: 63 - 64: 10.836 distance: 64 - 67: 14.509 distance: 65 - 66: 16.321 distance: 65 - 71: 9.877 distance: 67 - 68: 15.498 distance: 68 - 69: 11.392 distance: 68 - 70: 11.713 distance: 71 - 72: 5.831 distance: 71 - 77: 13.948 distance: 72 - 73: 13.075 distance: 72 - 75: 10.009 distance: 73 - 74: 21.285 distance: 73 - 78: 33.367 distance: 75 - 76: 15.653 distance: 76 - 77: 4.591 distance: 78 - 79: 21.691 distance: 79 - 80: 6.840 distance: 79 - 82: 14.313 distance: 80 - 81: 20.255 distance: 80 - 86: 20.136 distance: 82 - 83: 20.899 distance: 83 - 84: 15.201 distance: 83 - 85: 13.527 distance: 86 - 87: 5.916 distance: 86 - 92: 21.592 distance: 87 - 88: 12.661 distance: 87 - 90: 19.840 distance: 88 - 89: 3.020 distance: 88 - 93: 12.178 distance: 90 - 91: 6.248 distance: 91 - 92: 8.574 distance: 93 - 94: 14.423 distance: 94 - 95: 4.699 distance: 94 - 97: 10.074 distance: 95 - 96: 14.153 distance: 95 - 101: 6.156 distance: 97 - 98: 4.799 distance: 98 - 99: 14.869 distance: 98 - 100: 20.483 distance: 101 - 102: 4.630 distance: 102 - 103: 5.121 distance: 102 - 105: 10.800 distance: 103 - 104: 8.036 distance: 103 - 110: 8.133 distance: 105 - 106: 6.046 distance: 106 - 107: 12.476 distance: 107 - 108: 24.243 distance: 108 - 109: 8.283