Starting phenix.real_space_refine on Mon Feb 19 13:19:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/02_2024/8h14_34424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/02_2024/8h14_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_34424/02_2024/8h14_34424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/02_2024/8h14_34424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/02_2024/8h14_34424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h14_34424/02_2024/8h14_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-dev-5238/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: 12.30, per 1000 atoms: 0.50 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: 9.23 Conformation dependent library (CDL) restraints added in 3.9 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: 6.40 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: 9.85 Time building geometry restraints manager: 9.40 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: 0.890 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: 4.930 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 62.830 Find NCS groups from input model: 1.650 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.710 ------------------------------------------------------------------------------- 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 : 2.733 Fit side-chains REVERT: A 153 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6608 (p90) REVERT: A 758 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: A 851 MET cc_start: 0.8382 (mtt) cc_final: 0.8007 (mtt) REVERT: A 884 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8471 (mmp) REVERT: B 128 CYS cc_start: 0.6404 (t) cc_final: 0.6186 (t) REVERT: B 572 ASP cc_start: 0.7158 (m-30) cc_final: 0.6858 (m-30) REVERT: B 736 LEU cc_start: 0.8627 (tp) cc_final: 0.8358 (tp) REVERT: B 758 ARG cc_start: 0.7651 (ttp-110) cc_final: 0.7444 (ttp-110) REVERT: B 973 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.6985 (p) REVERT: C 153 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6518 (p90) REVERT: C 479 ASN cc_start: 0.8338 (t0) cc_final: 0.8019 (t0) REVERT: C 572 ASP cc_start: 0.7389 (m-30) cc_final: 0.6945 (m-30) REVERT: C 709 MET cc_start: 0.8705 (mtt) cc_final: 0.8209 (mtm) REVERT: C 740 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7462 (p) REVERT: C 1105 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8587 (m) outliers start: 36 outliers final: 13 residues processed: 278 average time/residue: 0.3964 time to fit residues: 173.9461 Evaluate side-chains 196 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 884 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.4980 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 79 optimal weight: 0.0070 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 A 883 GLN A 904 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 904 GLN C 939 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 25305 Z= 0.155 Angle : 0.508 8.021 34380 Z= 0.268 Chirality : 0.046 0.332 3990 Planarity : 0.004 0.041 4392 Dihedral : 7.410 58.358 4275 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.94 % Allowed : 6.18 % Favored : 92.88 % 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: -0.25 (0.14), residues: 3045 helix: 1.50 (0.21), residues: 666 sheet: 0.85 (0.19), residues: 744 loop : -1.44 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 423 HIS 0.002 0.000 HIS A1065 PHE 0.021 0.001 PHE A 130 TYR 0.016 0.001 TYR C1049 ARG 0.003 0.000 ARG B1089 *********************** 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 221 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7489 (t0) cc_final: 0.7043 (t0) REVERT: A 984 GLN cc_start: 0.7906 (tp40) cc_final: 0.7279 (tt0) REVERT: B 758 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.7307 (ttp-110) REVERT: B 960 ASN cc_start: 0.7610 (m-40) cc_final: 0.7231 (m-40) REVERT: C 295 ILE cc_start: 0.9073 (mm) cc_final: 0.8869 (mm) REVERT: C 1105 SER cc_start: 0.8936 (t) cc_final: 0.8666 (m) outliers start: 25 outliers final: 18 residues processed: 219 average time/residue: 0.3508 time to fit residues: 122.7741 Evaluate side-chains 190 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 0.0010 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 276 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.3768 ------------------------------------------------------------------------------- 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** A 917 GLN 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 904 GLN C 917 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: 0.8219 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25305 Z= 0.260 Angle : 0.556 11.407 34380 Z= 0.292 Chirality : 0.048 0.307 3990 Planarity : 0.004 0.037 4392 Dihedral : 6.619 54.995 4251 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.65 % Allowed : 8.20 % Favored : 90.15 % 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: -0.20 (0.14), residues: 3045 helix: 1.73 (0.21), residues: 651 sheet: 0.95 (0.19), residues: 714 loop : -1.47 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.003 0.001 HIS B1040 PHE 0.020 0.002 PHE A 83 TYR 0.022 0.001 TYR C1049 ARG 0.004 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 222 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 2.621 Fit side-chains REVERT: A 155 ASN cc_start: 0.7591 (t0) cc_final: 0.6230 (m-40) REVERT: A 984 GLN cc_start: 0.7846 (tp40) cc_final: 0.7528 (tt0) REVERT: B 758 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7559 (ttp-110) REVERT: C 274 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7700 (t0) REVERT: C 1105 SER cc_start: 0.8954 (t) cc_final: 0.8681 (m) outliers start: 44 outliers final: 29 residues processed: 216 average time/residue: 0.3696 time to fit residues: 128.8036 Evaluate side-chains 188 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 0.0670 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 279 optimal weight: 0.0770 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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** A 904 GLN B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 25305 Z= 0.163 Angle : 0.495 14.790 34380 Z= 0.258 Chirality : 0.045 0.286 3990 Planarity : 0.003 0.034 4392 Dihedral : 6.002 54.360 4250 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.20 % Allowed : 9.44 % Favored : 89.36 % 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: -0.05 (0.15), residues: 3045 helix: 1.78 (0.21), residues: 669 sheet: 1.04 (0.19), residues: 711 loop : -1.37 (0.13), residues: 1665 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 B 130 TYR 0.017 0.001 TYR A1049 ARG 0.001 0.000 ARG B 747 *********************** 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: 32 poor density : 173 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ILE cc_start: 0.8578 (mm) cc_final: 0.8267 (mm) REVERT: A 322 LEU cc_start: 0.8936 (tp) cc_final: 0.8725 (tp) REVERT: A 984 GLN cc_start: 0.7933 (tp40) cc_final: 0.7601 (tt0) REVERT: B 554 ASP cc_start: 0.7245 (m-30) cc_final: 0.6908 (m-30) REVERT: B 572 ASP cc_start: 0.7222 (m-30) cc_final: 0.6988 (m-30) REVERT: B 758 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.7322 (ttp-110) REVERT: C 428 ILE cc_start: 0.8721 (mm) cc_final: 0.8400 (mt) REVERT: C 1006 LEU cc_start: 0.9027 (tp) cc_final: 0.8815 (tp) outliers start: 32 outliers final: 26 residues processed: 199 average time/residue: 0.3737 time to fit residues: 119.4979 Evaluate side-chains 185 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 252 optimal weight: 0.0000 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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** A 904 GLN B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 25305 Z= 0.206 Angle : 0.508 14.179 34380 Z= 0.266 Chirality : 0.046 0.283 3990 Planarity : 0.004 0.034 4392 Dihedral : 5.770 50.561 4246 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.69 % Allowed : 10.15 % Favored : 88.16 % 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: -0.14 (0.14), residues: 3045 helix: 1.84 (0.21), residues: 669 sheet: 0.85 (0.20), residues: 621 loop : -1.30 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 423 HIS 0.002 0.000 HIS B1046 PHE 0.016 0.001 PHE A 130 TYR 0.019 0.001 TYR C1049 ARG 0.002 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 218 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 984 GLN cc_start: 0.7964 (tp40) cc_final: 0.7579 (tt0) REVERT: B 572 ASP cc_start: 0.7250 (m-30) cc_final: 0.7011 (m-30) REVERT: B 758 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7456 (ttp-110) REVERT: B 768 LYS cc_start: 0.7111 (ptpt) cc_final: 0.6298 (pttm) REVERT: C 274 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7647 (t0) outliers start: 45 outliers final: 41 residues processed: 212 average time/residue: 0.3626 time to fit residues: 123.2088 Evaluate side-chains 201 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG 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: 2.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** A 947 GLN B 181 HIS ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN C 889 ASN C 895 GLN C 939 GLN C 993 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25305 Z= 0.326 Angle : 0.582 13.545 34380 Z= 0.306 Chirality : 0.049 0.316 3990 Planarity : 0.004 0.037 4392 Dihedral : 6.066 55.130 4245 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.21 % Allowed : 10.75 % Favored : 87.04 % 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: -0.40 (0.14), residues: 3045 helix: 1.48 (0.21), residues: 687 sheet: 0.72 (0.20), residues: 624 loop : -1.45 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS B1046 PHE 0.023 0.002 PHE C 83 TYR 0.022 0.002 TYR C1049 ARG 0.004 0.000 ARG C 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 231 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 172 time to evaluate : 2.988 Fit side-chains revert: symmetry clash REVERT: A 768 LYS cc_start: 0.7702 (ptpt) cc_final: 0.6991 (pttm) REVERT: A 984 GLN cc_start: 0.8087 (tp40) cc_final: 0.7677 (tt0) REVERT: A 1105 SER cc_start: 0.8767 (t) cc_final: 0.8318 (m) REVERT: B 758 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7597 (ttp-110) REVERT: B 768 LYS cc_start: 0.7179 (ptpt) cc_final: 0.6355 (pttm) REVERT: C 274 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7659 (t0) REVERT: C 417 MET cc_start: 0.8824 (ttp) cc_final: 0.8285 (ttm) REVERT: C 992 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7793 (mm-40) outliers start: 59 outliers final: 51 residues processed: 223 average time/residue: 0.3698 time to fit residues: 131.3605 Evaluate side-chains 209 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 157 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 889 ASN Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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** C 896 ASN C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 25305 Z= 0.259 Angle : 0.545 16.150 34380 Z= 0.286 Chirality : 0.047 0.300 3990 Planarity : 0.004 0.037 4392 Dihedral : 5.959 55.042 4245 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.21 % Allowed : 11.50 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3045 helix: 1.53 (0.21), residues: 687 sheet: 0.70 (0.20), residues: 624 loop : -1.44 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.002 0.001 HIS B1046 PHE 0.017 0.001 PHE C 83 TYR 0.021 0.001 TYR C1049 ARG 0.003 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 227 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 168 time to evaluate : 2.741 Fit side-chains revert: symmetry clash REVERT: A 768 LYS cc_start: 0.7699 (ptpt) cc_final: 0.6984 (pttm) REVERT: A 984 GLN cc_start: 0.8031 (tp40) cc_final: 0.7629 (tt0) REVERT: B 758 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7576 (ttp-110) REVERT: B 768 LYS cc_start: 0.7134 (ptpt) cc_final: 0.6319 (pttm) REVERT: C 417 MET cc_start: 0.8891 (ttp) cc_final: 0.8380 (ttm) outliers start: 59 outliers final: 52 residues processed: 217 average time/residue: 0.3722 time to fit residues: 128.4326 Evaluate side-chains 210 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 158 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN C 939 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 25305 Z= 0.221 Angle : 0.530 15.607 34380 Z= 0.277 Chirality : 0.046 0.288 3990 Planarity : 0.004 0.036 4392 Dihedral : 5.806 54.964 4245 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.95 % Allowed : 12.17 % Favored : 85.88 % 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: -0.31 (0.14), residues: 3045 helix: 1.61 (0.21), residues: 687 sheet: 0.71 (0.20), residues: 624 loop : -1.39 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 868 HIS 0.002 0.001 HIS B1046 PHE 0.014 0.001 PHE A 130 TYR 0.019 0.001 TYR C1049 ARG 0.002 0.000 ARG B 965 *********************** 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 222 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 2.871 Fit side-chains revert: symmetry clash REVERT: A 642 VAL cc_start: 0.8404 (t) cc_final: 0.8023 (m) REVERT: A 768 LYS cc_start: 0.7689 (ptpt) cc_final: 0.6988 (pttm) REVERT: A 984 GLN cc_start: 0.7968 (tp40) cc_final: 0.7585 (tt0) REVERT: B 758 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7515 (ttp-110) REVERT: B 768 LYS cc_start: 0.7107 (ptpt) cc_final: 0.6266 (pttm) REVERT: C 572 ASP cc_start: 0.7456 (m-30) cc_final: 0.7231 (m-30) outliers start: 52 outliers final: 50 residues processed: 211 average time/residue: 0.3780 time to fit residues: 126.4676 Evaluate side-chains 215 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.9980 chunk 257 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2203 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= 0.179 Angle : 0.499 15.022 34380 Z= 0.260 Chirality : 0.045 0.296 3990 Planarity : 0.004 0.035 4392 Dihedral : 5.498 54.037 4245 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.69 % Allowed : 12.51 % Favored : 85.81 % 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: -0.22 (0.15), residues: 3045 helix: 1.73 (0.21), residues: 687 sheet: 0.72 (0.20), residues: 627 loop : -1.33 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 868 HIS 0.002 0.000 HIS B1065 PHE 0.013 0.001 PHE A 130 TYR 0.018 0.001 TYR A1049 ARG 0.002 0.000 ARG C 553 *********************** REFINEMENT MACRO_CYCLE 9 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 222 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 2.967 Fit side-chains revert: symmetry clash REVERT: A 642 VAL cc_start: 0.8396 (t) cc_final: 0.8021 (m) REVERT: A 768 LYS cc_start: 0.7667 (ptpt) cc_final: 0.6950 (pttm) REVERT: A 984 GLN cc_start: 0.7964 (tp40) cc_final: 0.7624 (tt0) REVERT: B 758 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7466 (ttp-110) REVERT: B 768 LYS cc_start: 0.7086 (ptpt) cc_final: 0.6262 (pttm) REVERT: C 572 ASP cc_start: 0.7405 (m-30) cc_final: 0.7005 (m-30) REVERT: C 1006 LEU cc_start: 0.9040 (tp) cc_final: 0.8836 (tp) outliers start: 45 outliers final: 44 residues processed: 211 average time/residue: 0.3551 time to fit residues: 119.6382 Evaluate side-chains 210 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 2.9990 chunk 177 optimal weight: 0.4980 chunk 137 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 304 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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** C 939 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25305 Z= 0.213 Angle : 0.518 15.142 34380 Z= 0.270 Chirality : 0.046 0.295 3990 Planarity : 0.004 0.035 4392 Dihedral : 5.498 54.629 4245 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.84 % Allowed : 12.51 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3045 helix: 1.77 (0.21), residues: 684 sheet: 0.73 (0.20), residues: 624 loop : -1.33 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 868 HIS 0.002 0.001 HIS B1046 PHE 0.014 0.001 PHE A 130 TYR 0.019 0.001 TYR C1049 ARG 0.002 0.000 ARG B 553 ********************** REFINEMENT MACRO_CYCLE 10 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 217 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 168 time to evaluate : 2.686 Fit side-chains revert: symmetry clash REVERT: A 642 VAL cc_start: 0.8409 (t) cc_final: 0.8035 (m) REVERT: A 768 LYS cc_start: 0.7672 (ptpt) cc_final: 0.6955 (pttm) REVERT: A 984 GLN cc_start: 0.7946 (tp40) cc_final: 0.7571 (tt0) REVERT: B 758 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7493 (ttp-110) REVERT: B 768 LYS cc_start: 0.7111 (ptpt) cc_final: 0.6280 (pttm) REVERT: C 572 ASP cc_start: 0.7416 (m-30) cc_final: 0.7011 (m-30) REVERT: C 848 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8512 (p) outliers start: 49 outliers final: 46 residues processed: 207 average time/residue: 0.3649 time to fit residues: 120.6048 Evaluate side-chains 213 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 166 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 969 CYS Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 0.2980 chunk 101 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** C 939 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.098857 restraints weight = 30936.062| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.70 r_work: 0.2759 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25305 Z= 0.282 Angle : 0.557 15.401 34380 Z= 0.290 Chirality : 0.048 0.300 3990 Planarity : 0.004 0.037 4392 Dihedral : 5.710 57.529 4245 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.95 % Allowed : 12.43 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3045 helix: 1.64 (0.21), residues: 684 sheet: 0.66 (0.20), residues: 624 loop : -1.38 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 868 HIS 0.002 0.001 HIS B1046 PHE 0.018 0.002 PHE C 83 TYR 0.021 0.001 TYR C1049 ARG 0.003 0.000 ARG B 747 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4341.51 seconds wall clock time: 80 minutes 38.61 seconds (4838.61 seconds total)