Starting phenix.real_space_refine on Wed Dec 13 03:20:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/12_2023/6zlt_11273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/12_2023/6zlt_11273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/12_2023/6zlt_11273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/12_2023/6zlt_11273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/12_2023/6zlt_11273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/12_2023/6zlt_11273.pdb" } resolution = 3.9 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 260 atoms to isotropic. 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 78 5.16 5 C 14766 2.51 5 N 3968 2.21 5 O 4574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ASP 615": "OD1" <-> "OD2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B GLU 818": "OE1" <-> "OE2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ASP 885": "OD1" <-> "OD2" Residue "B PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C ASP 409": "OD1" <-> "OD2" Residue "C ASP 453": "OD1" <-> "OD2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C ASP 471": "OD1" <-> "OD2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 537": "OD1" <-> "OD2" Residue "D TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ASP 614": "OD1" <-> "OD2" Residue "D ASP 615": "OD1" <-> "OD2" Residue "D GLU 629": "OE1" <-> "OE2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "D TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 747": "OE1" <-> "OE2" Residue "D GLU 774": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 826": "OE1" <-> "OE2" Residue "D ARG 834": "NH1" <-> "NH2" Residue "D ASP 885": "OD1" <-> "OD2" Residue "D PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 994": "OD1" <-> "OD2" Residue "D TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23386 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4358 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7335 Classifications: {'peptide': 933} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 900} Chain: "C" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4358 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7335 Classifications: {'peptide': 933} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 900} Time building chain proxies: 11.63, per 1000 atoms: 0.50 Number of scatterers: 23386 At special positions: 0 Unit cell: (155.15, 110.21, 140.17, 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 78 16.00 O 4574 8.00 N 3968 7.00 C 14766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 299 " distance=2.05 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 389 " distance=2.05 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 299 " distance=2.05 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 389 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.25 Conformation dependent library (CDL) restraints added in 4.0 seconds 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5396 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 28 sheets defined 22.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.738A pdb=" N ALA A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.332A pdb=" N ASP A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.906A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.910A pdb=" N HIS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.675A pdb=" N ASN A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.547A pdb=" N ILE A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP B 96 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 781 through 786 removed outlier: 3.814A pdb=" N GLY B 786 " --> pdb=" O VAL B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 914 removed outlier: 3.595A pdb=" N ASN B 913 " --> pdb=" O ARG B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 943 Processing helix chain 'B' and resid 961 through 967 Processing helix chain 'C' and resid 1 through 5 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.738A pdb=" N ALA C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 118 through 141 Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 185 removed outlier: 4.332A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.906A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 removed outlier: 3.910A pdb=" N HIS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 422 Processing helix chain 'C' and resid 426 through 442 Processing helix chain 'C' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS C 451 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 501 through 513 Processing helix chain 'C' and resid 517 through 521 removed outlier: 3.675A pdb=" N ASN C 521 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 542 removed outlier: 3.547A pdb=" N ILE C 539 " --> pdb=" O PRO C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP D 96 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU D 97 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 97' Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY D 113 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 377 through 384 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS D 608 " --> pdb=" O ASN D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 781 through 786 removed outlier: 3.814A pdb=" N GLY D 786 " --> pdb=" O VAL D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 822 Processing helix chain 'D' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 914 removed outlier: 3.595A pdb=" N ASN D 913 " --> pdb=" O ARG D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 943 Processing helix chain 'D' and resid 961 through 967 Processing sheet with id= 1, first strand: chain 'A' and resid 269 through 271 removed outlier: 4.076A pdb=" N TRP A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 405 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 271 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE A 403 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'B' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.363A pdb=" N ILE B 179 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 178 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 156 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE B 202 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE B 158 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 157 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 162 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 128 through 132 Processing sheet with id= 5, first strand: chain 'B' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR B 327 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 304 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 305 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 218 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B1012 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 220 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN B 953 " --> pdb=" O PHE B 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 873 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 745 " --> pdb=" O TYR B 711 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 711 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 749 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 706 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 712 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 627 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 617 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 626 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR B 591 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 574 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 514 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 554 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 508 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 506 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 509 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 490 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 488 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 221 through 224 Processing sheet with id= 7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG B 345 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.702A pdb=" N ARG B 426 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 452 " --> pdb=" O TRP B 483 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B 482 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS B 518 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA B 475 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE B 736 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 879 through 881 Processing sheet with id= 12, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.802A pdb=" N GLY B 264 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 273 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.606A pdb=" N GLU B 777 " --> pdb=" O ALA B 740 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 742 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE B 775 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN B 744 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B 773 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR B 853 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 806 " --> pdb=" O TRP B 851 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP B 851 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 269 through 271 removed outlier: 4.076A pdb=" N TRP C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE C 405 " --> pdb=" O TRP C 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 271 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE C 403 " --> pdb=" O ILE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'D' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR D 90 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 101 through 104 removed outlier: 4.363A pdb=" N ILE D 179 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 178 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 156 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE D 202 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE D 158 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 157 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 162 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 128 through 132 Processing sheet with id= 19, first strand: chain 'D' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR D 327 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL D 304 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 305 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 218 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D1012 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 220 " --> pdb=" O PHE D1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN D 953 " --> pdb=" O PHE D 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP D 873 " --> pdb=" O GLY D 957 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 760 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 745 " --> pdb=" O TYR D 711 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 711 " --> pdb=" O GLY D 745 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 749 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 706 " --> pdb=" O PHE D 697 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 712 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D 627 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 617 " --> pdb=" O ASP D 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY D 626 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR D 591 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 574 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 514 " --> pdb=" O TYR D 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 554 " --> pdb=" O ASN D 512 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY D 508 " --> pdb=" O PHE D 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET D 506 " --> pdb=" O LYS D 560 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET D 509 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 490 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 488 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 221 through 224 Processing sheet with id= 21, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG D 345 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.702A pdb=" N ARG D 426 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 452 " --> pdb=" O TRP D 483 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS D 482 " --> pdb=" O SER D 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS D 518 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA D 475 " --> pdb=" O THR D 460 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE D 736 " --> pdb=" O THR D 720 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 879 through 881 Processing sheet with id= 26, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.802A pdb=" N GLY D 264 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU D 273 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 740 through 744 removed outlier: 3.606A pdb=" N GLU D 777 " --> pdb=" O ALA D 740 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS D 742 " --> pdb=" O ILE D 775 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE D 775 " --> pdb=" O LYS D 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN D 744 " --> pdb=" O ASN D 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN D 773 " --> pdb=" O GLN D 744 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR D 853 " --> pdb=" O GLN D 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 806 " --> pdb=" O TRP D 851 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP D 851 " --> pdb=" O GLY D 806 " (cutoff:3.500A) 758 hydrogen bonds defined for protein. 2064 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: 9.49 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7760 1.34 - 1.47: 6076 1.47 - 1.59: 9968 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 23942 Sorted by residual: bond pdb=" N ASP C 300 " pdb=" CA ASP C 300 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.06e+00 bond pdb=" N ASP A 300 " pdb=" CA ASP A 300 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.06e+00 bond pdb=" C CYS C 298 " pdb=" N CYS C 299 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.47e+00 bond pdb=" C CYS A 298 " pdb=" N CYS A 299 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.47e+00 bond pdb=" CA LYS B 701 " pdb=" CB LYS B 701 " ideal model delta sigma weight residual 1.530 1.554 -0.023 1.51e-02 4.39e+03 2.41e+00 ... (remaining 23937 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.34: 516 106.34 - 113.29: 12204 113.29 - 120.25: 9120 120.25 - 127.20: 10422 127.20 - 134.15: 248 Bond angle restraints: 32510 Sorted by residual: angle pdb=" C CYS C 298 " pdb=" N CYS C 299 " pdb=" CA CYS C 299 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C CYS A 298 " pdb=" N CYS A 299 " pdb=" CA CYS A 299 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C GLY D 167 " pdb=" N MET D 168 " pdb=" CA MET D 168 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C GLY B 167 " pdb=" N MET B 168 " pdb=" CA MET B 168 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C ASP C 388 " pdb=" N CYS C 389 " pdb=" CA CYS C 389 " ideal model delta sigma weight residual 120.28 126.22 -5.94 1.44e+00 4.82e-01 1.70e+01 ... (remaining 32505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 12448 17.84 - 35.68: 1190 35.68 - 53.52: 270 53.52 - 71.36: 52 71.36 - 89.20: 32 Dihedral angle restraints: 13992 sinusoidal: 5446 harmonic: 8546 Sorted by residual: dihedral pdb=" CA CYS A 387 " pdb=" C CYS A 387 " pdb=" N ASP A 388 " pdb=" CA ASP A 388 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA CYS C 387 " pdb=" C CYS C 387 " pdb=" N ASP C 388 " pdb=" CA ASP C 388 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ALA D 566 " pdb=" C ALA D 566 " pdb=" N ASP D 567 " pdb=" CA ASP D 567 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 13989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2726 0.063 - 0.126: 570 0.126 - 0.189: 104 0.189 - 0.252: 10 0.252 - 0.315: 4 Chirality restraints: 3414 Sorted by residual: chirality pdb=" CB ILE D 212 " pdb=" CA ILE D 212 " pdb=" CG1 ILE D 212 " pdb=" CG2 ILE D 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE B 212 " pdb=" CA ILE B 212 " pdb=" CG1 ILE B 212 " pdb=" CG2 ILE B 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL B 668 " pdb=" CA VAL B 668 " pdb=" CG1 VAL B 668 " pdb=" CG2 VAL B 668 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 3411 not shown) Planarity restraints: 4290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 436 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 437 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 436 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 437 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 437 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 437 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 826 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" CD GLU B 826 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 826 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 826 " -0.013 2.00e-02 2.50e+03 ... (remaining 4287 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2136 2.74 - 3.28: 21776 3.28 - 3.82: 37984 3.82 - 4.36: 43678 4.36 - 4.90: 77374 Nonbonded interactions: 182948 Sorted by model distance: nonbonded pdb=" O THR A 324 " pdb=" OG1 THR A 324 " model vdw 2.198 2.440 nonbonded pdb=" O THR C 324 " pdb=" OG1 THR C 324 " model vdw 2.198 2.440 nonbonded pdb=" O SER A 55 " pdb=" OG SER A 55 " model vdw 2.215 2.440 nonbonded pdb=" O SER C 55 " pdb=" OG SER C 55 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR C 38 " pdb=" O SER D 653 " model vdw 2.252 2.440 ... (remaining 182943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 5.040 Check model and map are aligned: 0.420 Set scattering table: 0.220 Process input model: 59.670 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 0.048 23942 Z= 0.340 Angle : 0.817 9.596 32510 Z= 0.458 Chirality : 0.055 0.315 3414 Planarity : 0.006 0.056 4290 Dihedral : 15.478 89.199 8584 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.98 % Allowed : 10.99 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -4.15 (0.13), residues: 2962 helix: -2.67 (0.14), residues: 634 sheet: -2.81 (0.17), residues: 760 loop : -2.74 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 599 HIS 0.007 0.001 HIS D 482 PHE 0.025 0.002 PHE B 438 TYR 0.028 0.002 TYR B 191 ARG 0.004 0.000 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 295 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 315 average time/residue: 0.3993 time to fit residues: 190.4419 Evaluate side-chains 182 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3459 time to fit residues: 6.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 232 optimal weight: 0.0000 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 134 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 422 ASN A 506 ASN B 112 GLN B 115 ASN B 174 ASN B 233 ASN B 266 ASN B 347 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B 765 ASN B 816 GLN C 121 GLN C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN C 422 ASN C 506 ASN D 112 GLN D 115 ASN D 174 ASN ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 347 ASN D 603 GLN D 628 GLN ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN D 765 ASN D 816 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23942 Z= 0.224 Angle : 0.567 12.454 32510 Z= 0.304 Chirality : 0.043 0.148 3414 Planarity : 0.004 0.047 4290 Dihedral : 5.058 34.932 3278 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.69 % Allowed : 16.08 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.14), residues: 2962 helix: -0.92 (0.19), residues: 652 sheet: -2.20 (0.18), residues: 764 loop : -2.29 (0.14), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 599 HIS 0.004 0.001 HIS B 169 PHE 0.017 0.001 PHE C 135 TYR 0.020 0.001 TYR D 191 ARG 0.006 0.001 ARG D 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 204 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 40 residues processed: 257 average time/residue: 0.3509 time to fit residues: 144.2726 Evaluate side-chains 213 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 2.784 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2373 time to fit residues: 20.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 GLN ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 23942 Z= 0.349 Angle : 0.601 12.113 32510 Z= 0.324 Chirality : 0.044 0.163 3414 Planarity : 0.004 0.042 4290 Dihedral : 5.075 32.497 3278 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.14 % Allowed : 17.83 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.15), residues: 2962 helix: -0.29 (0.21), residues: 656 sheet: -1.95 (0.18), residues: 762 loop : -2.15 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 599 HIS 0.007 0.002 HIS B 518 PHE 0.019 0.001 PHE A 312 TYR 0.026 0.001 TYR D 191 ARG 0.004 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 182 time to evaluate : 2.700 Fit side-chains outliers start: 77 outliers final: 47 residues processed: 242 average time/residue: 0.3388 time to fit residues: 134.3656 Evaluate side-chains 214 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2222 time to fit residues: 22.9808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.6980 chunk 202 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 23942 Z= 0.209 Angle : 0.537 15.968 32510 Z= 0.286 Chirality : 0.042 0.139 3414 Planarity : 0.003 0.042 4290 Dihedral : 4.707 33.301 3278 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.55 % Allowed : 20.44 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2962 helix: 0.03 (0.21), residues: 654 sheet: -1.67 (0.19), residues: 766 loop : -1.96 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 599 HIS 0.004 0.001 HIS B 169 PHE 0.013 0.001 PHE C 135 TYR 0.016 0.001 TYR D 422 ARG 0.003 0.000 ARG D 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 2.612 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 218 average time/residue: 0.3575 time to fit residues: 126.1437 Evaluate side-chains 194 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2285 time to fit residues: 12.6776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 23942 Z= 0.487 Angle : 0.675 11.613 32510 Z= 0.363 Chirality : 0.046 0.189 3414 Planarity : 0.004 0.042 4290 Dihedral : 5.278 32.611 3278 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.65 % Allowed : 21.58 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 2962 helix: 0.23 (0.22), residues: 618 sheet: -1.85 (0.19), residues: 742 loop : -2.02 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 599 HIS 0.009 0.002 HIS D 518 PHE 0.019 0.002 PHE D 342 TYR 0.034 0.002 TYR D 191 ARG 0.005 0.001 ARG D 974 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 185 time to evaluate : 3.488 Fit side-chains outliers start: 65 outliers final: 32 residues processed: 233 average time/residue: 0.3474 time to fit residues: 134.3242 Evaluate side-chains 204 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2291 time to fit residues: 17.5159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 167 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 286 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23942 Z= 0.142 Angle : 0.521 12.151 32510 Z= 0.276 Chirality : 0.042 0.139 3414 Planarity : 0.003 0.039 4290 Dihedral : 4.595 31.543 3278 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.86 % Allowed : 23.25 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.15), residues: 2962 helix: 0.23 (0.22), residues: 654 sheet: -1.42 (0.19), residues: 736 loop : -1.78 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 599 HIS 0.003 0.001 HIS C 132 PHE 0.011 0.001 PHE C 135 TYR 0.017 0.001 TYR D 422 ARG 0.003 0.000 ARG D 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 2.538 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 203 average time/residue: 0.3504 time to fit residues: 115.2397 Evaluate side-chains 178 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2630 time to fit residues: 6.0162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 0.0060 chunk 241 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 285 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 173 optimal weight: 0.0870 chunk 131 optimal weight: 10.0000 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23942 Z= 0.122 Angle : 0.519 17.137 32510 Z= 0.272 Chirality : 0.042 0.200 3414 Planarity : 0.003 0.058 4290 Dihedral : 4.346 47.033 3278 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.86 % Allowed : 24.31 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 2962 helix: 0.20 (0.21), residues: 668 sheet: -1.10 (0.20), residues: 738 loop : -1.68 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 599 HIS 0.003 0.001 HIS C 132 PHE 0.010 0.001 PHE C 135 TYR 0.016 0.001 TYR B 771 ARG 0.009 0.000 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 2.769 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 210 average time/residue: 0.3540 time to fit residues: 120.0590 Evaluate side-chains 181 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 2.835 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2479 time to fit residues: 7.4163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 8.9990 chunk 113 optimal weight: 0.0000 chunk 170 optimal weight: 4.9990 chunk 85 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23942 Z= 0.166 Angle : 0.540 19.406 32510 Z= 0.280 Chirality : 0.042 0.191 3414 Planarity : 0.003 0.038 4290 Dihedral : 4.322 43.216 3278 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.86 % Allowed : 25.16 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 2962 helix: 0.26 (0.21), residues: 668 sheet: -1.01 (0.20), residues: 738 loop : -1.62 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 599 HIS 0.004 0.001 HIS C 132 PHE 0.010 0.001 PHE D 342 TYR 0.018 0.001 TYR B 771 ARG 0.010 0.000 ARG B 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 2.654 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 190 average time/residue: 0.3726 time to fit residues: 114.3221 Evaluate side-chains 182 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 2.551 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2337 time to fit residues: 8.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 7.9990 chunk 273 optimal weight: 0.0010 chunk 249 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 23942 Z= 0.150 Angle : 0.539 21.182 32510 Z= 0.278 Chirality : 0.042 0.154 3414 Planarity : 0.003 0.041 4290 Dihedral : 4.235 38.893 3278 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.49 % Allowed : 25.04 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2962 helix: 0.30 (0.21), residues: 668 sheet: -0.89 (0.20), residues: 744 loop : -1.56 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 599 HIS 0.005 0.001 HIS C 132 PHE 0.020 0.001 PHE A 312 TYR 0.018 0.001 TYR B 771 ARG 0.010 0.000 ARG B 832 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 2.799 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 182 average time/residue: 0.3651 time to fit residues: 107.7163 Evaluate side-chains 175 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2450 time to fit residues: 6.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1455 > 50: distance: 40 - 46: 25.935 distance: 46 - 47: 26.222 distance: 47 - 48: 21.824 distance: 47 - 50: 42.550 distance: 48 - 49: 35.398 distance: 48 - 51: 35.205 distance: 51 - 52: 34.183 distance: 52 - 53: 17.670 distance: 52 - 55: 5.471 distance: 53 - 54: 32.246 distance: 53 - 60: 25.458 distance: 55 - 56: 12.136 distance: 56 - 57: 19.656 distance: 57 - 58: 13.872 distance: 57 - 59: 7.409 distance: 60 - 61: 12.828 distance: 61 - 62: 10.832 distance: 61 - 64: 3.583 distance: 62 - 63: 11.676 distance: 62 - 67: 14.617 distance: 64 - 65: 23.326 distance: 64 - 66: 14.155 distance: 67 - 68: 21.700 distance: 68 - 69: 10.871 distance: 68 - 71: 13.836 distance: 69 - 70: 13.644 distance: 69 - 72: 11.133 distance: 72 - 73: 24.565 distance: 73 - 74: 15.512 distance: 73 - 76: 10.993 distance: 74 - 75: 21.267 distance: 74 - 79: 51.966 distance: 76 - 77: 11.669 distance: 76 - 78: 24.855 distance: 79 - 80: 14.190 distance: 80 - 81: 21.940 distance: 80 - 83: 41.002 distance: 81 - 82: 21.768 distance: 81 - 87: 33.674 distance: 83 - 84: 27.916 distance: 84 - 85: 9.529 distance: 84 - 86: 26.205 distance: 87 - 88: 10.161 distance: 88 - 89: 23.241 distance: 88 - 91: 37.400 distance: 89 - 90: 12.106 distance: 89 - 92: 21.486 distance: 92 - 93: 32.122 distance: 93 - 94: 28.476 distance: 93 - 96: 40.594 distance: 94 - 95: 37.341 distance: 94 - 99: 7.624 distance: 96 - 97: 33.585 distance: 96 - 98: 31.695 distance: 99 - 100: 8.346 distance: 100 - 101: 28.048 distance: 100 - 103: 19.163 distance: 101 - 102: 24.909 distance: 101 - 107: 20.649 distance: 103 - 104: 29.645 distance: 104 - 105: 9.693 distance: 104 - 106: 23.439 distance: 107 - 108: 12.482 distance: 107 - 113: 19.181 distance: 108 - 109: 23.771 distance: 108 - 111: 23.973 distance: 109 - 110: 26.589 distance: 109 - 114: 6.635 distance: 111 - 112: 25.439 distance: 112 - 113: 22.986