Starting phenix.real_space_refine (version: dev) on Wed Feb 22 19:53:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/02_2023/6ue9_20751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/02_2023/6ue9_20751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/02_2023/6ue9_20751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/02_2023/6ue9_20751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/02_2023/6ue9_20751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/02_2023/6ue9_20751.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.013 sd= 0.420 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 Process input model Symmetric amino acids flipped Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "G ARG 346": "NH1" <-> "NH2" Residue "G ASP 378": "OD1" <-> "OD2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "G TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K GLU 358": "OE1" <-> "OE2" Residue "L GLU 389": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18227 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1686 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4150 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 511} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1038 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1656 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1666 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1570 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1556 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 103 Chain: "K" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1581 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1543 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.17, per 1000 atoms: 0.56 Number of scatterers: 18227 At special positions: 0 Unit cell: (173.196, 148.745, 174.215, 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 98 16.00 O 3490 8.00 N 3151 7.00 C 11488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.05 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.04 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 311 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.02 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.05 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.04 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.04 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 471 " - pdb=" SG CYS E 471 " distance=2.03 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS H 299 " distance=2.04 Simple disulfide: pdb=" SG CYS E 299 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 369 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 323 " distance=2.04 Simple disulfide: pdb=" SG CYS H 369 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 242 " - pdb=" SG CYS L 299 " distance=2.04 Simple disulfide: pdb=" SG CYS K 266 " - pdb=" SG CYS K 323 " distance=2.04 Simple disulfide: pdb=" SG CYS K 299 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 369 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 266 " - pdb=" SG CYS L 323 " distance=2.04 Simple disulfide: pdb=" SG CYS L 369 " - pdb=" SG CYS L 432 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 337 " " NAG B 501 " - " ASN B 337 " " NAG C 601 " - " ASN C 403 " " NAG C 604 " - " ASN C 65 " " NAG C 605 " - " ASN C 451 " " NAG F 501 " - " ASN F 337 " " NAG G 501 " - " ASN G 337 " " NAG I 1 " - " ASN C 72 " " NAG J 1 " - " ASN D 49 " Time building additional restraints: 5.87 Conformation dependent library (CDL) restraints added in 2.6 seconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4598 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 55 sheets defined 9.7% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.616A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.828A pdb=" N ASN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.759A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.611A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.608A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.603A pdb=" N GLU B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 359' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.741A pdb=" N LYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.652A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.777A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 246' Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.691A pdb=" N PHE C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.775A pdb=" N ASP C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 302 " --> pdb=" O LYS C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.631A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.535A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.637A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.661A pdb=" N LEU F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.587A pdb=" N GLY F 318 " --> pdb=" O PRO F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 421 through 427 removed outlier: 3.698A pdb=" N LYS F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.548A pdb=" N LEU G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 removed outlier: 4.320A pdb=" N GLY G 300 " --> pdb=" O ASP G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'G' and resid 420 through 427 removed outlier: 3.615A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.697A pdb=" N ASN E 316 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.522A pdb=" N ALA E 360 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.763A pdb=" N LEU H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 317 removed outlier: 3.552A pdb=" N ASN H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.828A pdb=" N LEU H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN H 362 " --> pdb=" O GLU H 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 357 through 362' Processing helix chain 'H' and resid 421 through 427 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 297 through 301 removed outlier: 4.539A pdb=" N GLY K 300 " --> pdb=" O ASP K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 318 Processing helix chain 'K' and resid 356 through 360 Processing helix chain 'K' and resid 421 through 427 Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.713A pdb=" N ALA L 360 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 426 removed outlier: 3.931A pdb=" N TRP L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA6, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.304A pdb=" N ILE K 458 " --> pdb=" O ASN L 459 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER L 461 " --> pdb=" O ILE K 458 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL K 460 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL L 463 " --> pdb=" O VAL K 460 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 462 " --> pdb=" O VAL L 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.759A pdb=" N SER B 247 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 267 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 265 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 308 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR B 267 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 306 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR B 269 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL B 304 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 320 through 325 removed outlier: 3.517A pdb=" N ALA B 325 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.453A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.575A pdb=" N ILE C 79 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 125 removed outlier: 6.571A pdb=" N TYR C 122 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU C 220 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.559A pdb=" N LEU C 201 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 225 through 229 removed outlier: 6.123A pdb=" N GLU C 225 " --> pdb=" O GLN C 325 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE C 327 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 227 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 239 Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.260A pdb=" N VAL C 341 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 440 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C 343 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 381 " --> pdb=" O TRP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 349 through 354 removed outlier: 3.517A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 408 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC4, first strand: chain 'C' and resid 474 through 479 removed outlier: 3.775A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 525 " --> pdb=" O CYS C 478 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 533 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 11 removed outlier: 5.460A pdb=" N VAL D 7 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER D 20 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN E 459 " --> pdb=" O VAL H 460 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL H 462 " --> pdb=" O ASN E 459 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER E 461 " --> pdb=" O VAL H 462 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AC7, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AC8, first strand: chain 'F' and resid 245 through 249 removed outlier: 3.651A pdb=" N ARG F 245 " --> pdb=" O THR F 269 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 269 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY F 270 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR F 302 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 324 through 325 Processing sheet with id=AD1, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AD4, first strand: chain 'G' and resid 245 through 249 removed outlier: 3.744A pdb=" N ARG G 245 " --> pdb=" O THR G 269 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS G 249 " --> pdb=" O THR G 265 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR G 265 " --> pdb=" O HIS G 249 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 264 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 278 through 281 Processing sheet with id=AD6, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD9, first strand: chain 'E' and resid 245 through 248 removed outlier: 4.240A pdb=" N ARG E 245 " --> pdb=" O THR E 269 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 269 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 268 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLY E 270 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR E 302 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 290 through 291 removed outlier: 4.622A pdb=" N VAL E 290 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL E 307 " --> pdb=" O VAL E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 396 " --> pdb=" O ILE E 416 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AE5, first strand: chain 'E' and resid 384 through 385 Processing sheet with id=AE6, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.505A pdb=" N ARG H 245 " --> pdb=" O THR H 269 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 269 " --> pdb=" O ARG H 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 280 through 281 Processing sheet with id=AE8, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AE9, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 388 through 389 Processing sheet with id=AF3, first strand: chain 'K' and resid 246 through 248 removed outlier: 4.076A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 290 " --> pdb=" O VAL K 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 278 through 281 removed outlier: 3.642A pdb=" N THR K 278 " --> pdb=" O ALA K 326 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU K 396 " --> pdb=" O ILE K 416 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR K 410 " --> pdb=" O GLU K 403 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.526A pdb=" N SER K 431 " --> pdb=" O LEU K 384 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.951A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU L 370 " --> pdb=" O HIS L 350 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU L 352 " --> pdb=" O THR L 368 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU L 396 " --> pdb=" O ILE L 416 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 388 through 389 removed outlier: 3.637A pdb=" N GLN L 388 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 385 " --> pdb=" O GLN L 388 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 382 " --> pdb=" O MET L 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 401 through 403 removed outlier: 3.692A pdb=" N ARG L 401 " --> pdb=" O ALA L 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 412 " --> pdb=" O ARG L 401 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR L 410 " --> pdb=" O GLU L 403 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1452 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: 6.07 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5888 1.34 - 1.46: 4375 1.46 - 1.59: 8280 1.59 - 1.71: 0 1.71 - 1.84: 115 Bond restraints: 18658 Sorted by residual: bond pdb=" C THR D 54 " pdb=" N SER D 55 " ideal model delta sigma weight residual 1.327 1.300 0.027 1.05e-02 9.07e+03 6.40e+00 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.10e-02 8.26e+03 5.80e+00 bond pdb=" C GLN E 313 " pdb=" N PRO E 314 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.51e+00 bond pdb=" C7 NAG J 2 " pdb=" N2 NAG J 2 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.10e-02 8.26e+03 5.06e+00 bond pdb=" N GLU G 358 " pdb=" CA GLU G 358 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.89e+00 ... (remaining 18653 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.87: 622 105.87 - 112.95: 10424 112.95 - 120.03: 5896 120.03 - 127.11: 8327 127.11 - 134.20: 317 Bond angle restraints: 25586 Sorted by residual: angle pdb=" N SER D 55 " pdb=" CA SER D 55 " pdb=" C SER D 55 " ideal model delta sigma weight residual 108.13 99.01 9.12 9.00e-01 1.23e+00 1.03e+02 angle pdb=" C2 NAG J 2 " pdb=" N2 NAG J 2 " pdb=" C7 NAG J 2 " ideal model delta sigma weight residual 123.12 134.20 -11.08 1.28e+00 6.08e-01 7.45e+01 angle pdb=" C2 NAG A 501 " pdb=" N2 NAG A 501 " pdb=" C7 NAG A 501 " ideal model delta sigma weight residual 123.12 133.97 -10.85 1.28e+00 6.08e-01 7.16e+01 angle pdb=" C ASN C 329 " pdb=" N GLU C 330 " pdb=" CA GLU C 330 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C GLY A 453 " pdb=" N LYS A 454 " pdb=" CA LYS A 454 " ideal model delta sigma weight residual 120.39 127.45 -7.06 1.39e+00 5.18e-01 2.58e+01 ... (remaining 25581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.32: 10200 19.32 - 38.64: 822 38.64 - 57.96: 115 57.96 - 77.28: 14 77.28 - 96.60: 9 Dihedral angle restraints: 11160 sinusoidal: 4056 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS K 299 " pdb=" SG CYS K 299 " pdb=" SG CYS L 242 " pdb=" CB CYS L 242 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 323 " pdb=" CB CYS H 323 " ideal model delta sinusoidal sigma weight residual 93.00 3.83 89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual -86.00 -158.33 72.33 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 11157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2658 0.085 - 0.170: 382 0.170 - 0.254: 31 0.254 - 0.339: 4 0.339 - 0.424: 5 Chirality restraints: 3080 Sorted by residual: chirality pdb=" C1 NAG C 605 " pdb=" ND2 ASN C 451 " pdb=" C2 NAG C 605 " pdb=" O5 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CB ILE E 448 " pdb=" CA ILE E 448 " pdb=" CG1 ILE E 448 " pdb=" CG2 ILE E 448 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 3077 not shown) Planarity restraints: 3287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 403 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO F 404 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 404 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 404 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 327 " -0.046 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO B 328 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 375 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO L 376 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 376 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 376 " 0.039 5.00e-02 4.00e+02 ... (remaining 3284 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3153 2.77 - 3.30: 14380 3.30 - 3.84: 26867 3.84 - 4.37: 28681 4.37 - 4.90: 54365 Nonbonded interactions: 127446 Sorted by model distance: nonbonded pdb=" OG1 THR H 282 " pdb=" OG1 THR H 322 " model vdw 2.241 2.440 nonbonded pdb=" O THR H 280 " pdb=" OG1 THR H 324 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR L 320 " pdb=" OD1 ASN L 337 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR C 122 " pdb=" OD1 ASN C 133 " model vdw 2.292 2.440 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.318 2.520 ... (remaining 127441 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 242 through 244 or (resid 245 and (name N or name CA or na \ me C or name O or name CB )) or resid 246 through 253 or (resid 254 through 255 \ and (name N or name CA or name C or name O or name CB )) or resid 256 through 25 \ 9 or (resid 260 through 262 and (name N or name CA or name C or name O or name C \ B )) or resid 263 through 270 or (resid 271 through 272 and (name N or name CA o \ r name C or name O or name CB )) or resid 276 through 286 or (resid 287 and (nam \ e N or name CA or name C or name O or name CB )) or resid 288 through 312 or (re \ sid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB )) or resid 342 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 through \ 363 and (name N or name CA or name C or name O or name CB )) or resid 364 throug \ h 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) or \ resid 378 through 387 or (resid 388 and (name N or name CA or name C or name O o \ r name CB )) or resid 389 through 391 or (resid 392 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 404 or (resid 405 \ through 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 through 424 or (resid 425 through 426 and (name N or name CA or name C or name \ O or name CB )) or resid 427 or (resid 428 and (name N or name CA or name C or \ name O or name CB )) or resid 429 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 456 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 295 or (resid 296 through 298 and (name N or name CA or n \ ame C or name O or name CB )) or resid 299 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB )) or resid 314 through 340 or (resid \ 341 and (name N or name CA or name C or name O or name CB )) or resid 342 throu \ gh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 356 or (resid 357 through 363 and (name N or name CA or name \ C or name O or name CB )) or resid 364 through 376 or (resid 377 and (name N or \ name CA or name C or name O or name CB )) or resid 378 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 3 \ 91 or (resid 392 through 394 and (name N or name CA or name C or name O or name \ CB )) or resid 395 through 404 or (resid 405 through 406 and (name N or name CA \ or name C or name O or name CB )) or resid 407 through 424 or (resid 425 through \ 426 and (name N or name CA or name C or name O or name CB )) or resid 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 t \ hrough 445 or (resid 446 and (name N or name CA or name C or name O or name CB ) \ ) or resid 447 through 449 or (resid 450 and (name N or name CA or name C or nam \ e O or name CB )) or resid 456 through 464)) selection = (chain 'E' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 450 o \ r resid 456 through 464)) selection = (chain 'F' and (resid 242 through 259 or (resid 260 through 262 and (name N or n \ ame CA or name C or name O or name CB )) or resid 263 through 272 or resid 276 t \ hrough 310 or (resid 311 through 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 340 or (resid 341 and (name N or name CA or n \ ame C or name O or name CB )) or resid 342 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 356 or (resid \ 357 through 363 and (name N or name CA or name C or name O or name CB )) or res \ id 364 through 376 or (resid 377 and (name N or name CA or name C or name O or n \ ame CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 and \ (name N or name CA or name C or name O or name CB )) or resid 395 through 404 o \ r (resid 405 through 406 and (name N or name CA or name C or name O or name CB ) \ ) or resid 407 through 424 or (resid 425 through 426 and (name N or name CA or n \ ame C or name O or name CB )) or resid 427 through 445 or (resid 446 and (name N \ or name CA or name C or name O or name CB )) or resid 447 through 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 456 throu \ gh 464)) selection = (chain 'G' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 316 or (resid 317 and (name N or name CA or name C or nam \ e O or name CB )) or resid 318 through 340 or (resid 341 and (name N or name CA \ or name C or name O or name CB )) or resid 342 through 345 or (resid 346 and (na \ me N or name CA or name C or name O or name CB )) or resid 347 through 356 or (r \ esid 357 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 376 or (resid 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 \ and (name N or name CA or name C or name O or name CB )) or resid 395 through 4 \ 04 or (resid 405 through 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 424 or (resid 425 through 426 and (na \ me N or name CA or name C or name O or name CB )) or resid 427 through 445 or (r \ esid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 t \ hrough 449 or (resid 450 and (name N or name CA or name C or name O or name CB ) \ ) or resid 456 through 464)) selection = (chain 'H' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 312 o \ r (resid 313 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 14 through 424 or (resid 425 through 426 and (name N or name CA or name C or nam \ e O or name CB )) or resid 427 through 450 or resid 456 through 464)) selection = (chain 'K' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 312 or (resid 313 and (name N or name CA or name C or nam \ e O or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA \ or name C or name O or name CB )) or resid 318 through 340 or (resid 341 and (na \ me N or name CA or name C or name O or name CB )) or resid 342 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 356 or (resid 357 through 363 and (name N or name CA or name C or name O \ or name CB )) or resid 364 through 376 or (resid 377 and (name N or name CA or n \ ame C or name O or name CB )) or resid 378 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 392 or (resid \ 393 through 394 and (name N or name CA or name C or name O or name CB )) or res \ id 395 through 404 or (resid 405 through 406 and (name N or name CA or name C or \ name O or name CB )) or resid 407 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 450 or resid 456 thro \ ugh 464)) selection = (chain 'L' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 345 or (resid 346 and (name N or name CA or name C or nam \ e O or name CB )) or resid 347 through 358 or (resid 359 through 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 376 or (resid \ 377 and (name N or name CA or name C or name O or name CB )) or resid 378 throu \ gh 392 or (resid 393 through 394 and (name N or name CA or name C or name O or n \ ame CB )) or resid 395 through 425 or (resid 426 and (name N or name CA or name \ C or name O or name CB )) or resid 427 through 450 or resid 456 through 464)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 11488 2.51 5 N 3151 2.21 5 O 3490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 13.930 Check model and map are aligned: 0.260 Process input model: 44.900 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3738 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 : 0.007 0.072 18658 Z= 0.441 Angle : 1.042 16.113 25586 Z= 0.566 Chirality : 0.061 0.424 3080 Planarity : 0.008 0.075 3278 Dihedral : 13.760 96.601 6451 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.14), residues: 2439 helix: -4.23 (0.21), residues: 143 sheet: -1.61 (0.16), residues: 863 loop : -3.14 (0.13), residues: 1433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 539 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 544 average time/residue: 0.9539 time to fit residues: 597.9457 Evaluate side-chains 261 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.2511 time to fit residues: 3.7405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 291 GLN B 406 GLN C 209 ASN D 11 ASN D 30 ASN D 37 ASN D 90 ASN F 362 ASN F 459 ASN G 263 ASN G 291 GLN ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN E 327 HIS E 459 ASN H 243 HIS H 249 HIS H 316 ASN ** H 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN K 243 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4871 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 18658 Z= 0.308 Angle : 0.933 13.909 25586 Z= 0.451 Chirality : 0.050 0.316 3080 Planarity : 0.007 0.064 3278 Dihedral : 6.985 99.234 2674 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 7.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.15), residues: 2439 helix: -3.35 (0.28), residues: 143 sheet: -0.86 (0.17), residues: 822 loop : -2.74 (0.14), residues: 1474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 341 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 56 residues processed: 444 average time/residue: 0.8247 time to fit residues: 434.0764 Evaluate side-chains 323 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 267 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 37 residues processed: 19 average time/residue: 0.2516 time to fit residues: 10.2904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN C 530 GLN F 327 HIS ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS H 316 ASN ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.9001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.270 18658 Z= 0.519 Angle : 1.115 16.482 25586 Z= 0.560 Chirality : 0.058 0.461 3080 Planarity : 0.008 0.128 3278 Dihedral : 7.150 97.714 2674 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.98 % Favored : 90.98 % Rotamer Outliers : 11.13 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.80 (0.15), residues: 2439 helix: -2.54 (0.33), residues: 159 sheet: -0.75 (0.18), residues: 791 loop : -2.54 (0.14), residues: 1489 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 430 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 209 outliers final: 81 residues processed: 584 average time/residue: 0.8850 time to fit residues: 605.2089 Evaluate side-chains 407 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 326 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 67 residues processed: 17 average time/residue: 0.1963 time to fit residues: 8.9409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 115 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 236 optimal weight: 0.2980 chunk 116 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 343 ASN C 78 ASN D 88 GLN F 243 HIS F 316 ASN F 457 HIS H 243 HIS ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 HIS K 445 GLN K 457 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 1.0302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 18658 Z= 0.292 Angle : 0.893 17.564 25586 Z= 0.423 Chirality : 0.048 0.320 3080 Planarity : 0.006 0.056 3278 Dihedral : 6.371 100.478 2674 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 10.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.35 (0.16), residues: 2439 helix: -1.68 (0.39), residues: 144 sheet: -0.47 (0.18), residues: 791 loop : -2.28 (0.14), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 354 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 96 residues processed: 485 average time/residue: 0.9065 time to fit residues: 514.0046 Evaluate side-chains 399 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 303 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 73 residues processed: 29 average time/residue: 0.2022 time to fit residues: 12.8685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 150 GLN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN F 457 HIS ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 GLN E 263 ASN H 243 HIS ** K 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 HIS K 457 HIS L 249 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 1.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 18658 Z= 0.385 Angle : 0.957 23.719 25586 Z= 0.463 Chirality : 0.051 0.345 3080 Planarity : 0.006 0.093 3278 Dihedral : 6.532 99.444 2674 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 9.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.26 (0.16), residues: 2439 helix: -1.71 (0.39), residues: 165 sheet: -0.46 (0.18), residues: 819 loop : -2.20 (0.15), residues: 1455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 338 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 178 outliers final: 84 residues processed: 468 average time/residue: 1.0033 time to fit residues: 545.6723 Evaluate side-chains 361 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 277 time to evaluate : 2.168 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 68 residues processed: 17 average time/residue: 0.4216 time to fit residues: 12.7856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN C 78 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** G 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS H 445 GLN K 291 GLN K 457 HIS L 385 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 1.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 18658 Z= 0.243 Angle : 0.844 23.018 25586 Z= 0.398 Chirality : 0.046 0.327 3080 Planarity : 0.005 0.058 3278 Dihedral : 6.096 99.474 2674 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 7.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.02 (0.16), residues: 2439 helix: -1.47 (0.40), residues: 159 sheet: -0.31 (0.18), residues: 821 loop : -2.04 (0.15), residues: 1459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 317 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 87 residues processed: 418 average time/residue: 1.0052 time to fit residues: 483.8066 Evaluate side-chains 361 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 274 time to evaluate : 2.232 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 87 outliers final: 72 residues processed: 19 average time/residue: 0.2363 time to fit residues: 9.8868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 HIS F 343 ASN H 243 HIS K 457 HIS L 385 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 1.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 18658 Z= 0.314 Angle : 0.881 23.660 25586 Z= 0.418 Chirality : 0.047 0.337 3080 Planarity : 0.005 0.058 3278 Dihedral : 6.124 99.892 2674 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 7.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.95 (0.16), residues: 2439 helix: -1.37 (0.41), residues: 157 sheet: -0.26 (0.18), residues: 814 loop : -1.99 (0.15), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 285 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 91 residues processed: 393 average time/residue: 0.9846 time to fit residues: 447.3727 Evaluate side-chains 341 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 250 time to evaluate : 2.076 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 91 outliers final: 73 residues processed: 19 average time/residue: 0.2830 time to fit residues: 10.9944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 150 optimal weight: 0.0770 chunk 160 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 291 GLN ** G 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS H 445 GLN K 249 HIS K 457 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 1.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 18658 Z= 0.230 Angle : 0.852 22.849 25586 Z= 0.401 Chirality : 0.046 0.323 3080 Planarity : 0.005 0.058 3278 Dihedral : 5.889 99.559 2674 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 5.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.81 (0.16), residues: 2439 helix: -1.26 (0.41), residues: 156 sheet: -0.14 (0.18), residues: 824 loop : -1.92 (0.15), residues: 1459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 276 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 86 residues processed: 370 average time/residue: 1.0212 time to fit residues: 436.7458 Evaluate side-chains 343 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 257 time to evaluate : 1.964 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 86 outliers final: 77 residues processed: 11 average time/residue: 0.2486 time to fit residues: 6.9883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 GLN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS K 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 1.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 18658 Z= 0.340 Angle : 0.919 23.522 25586 Z= 0.440 Chirality : 0.048 0.351 3080 Planarity : 0.006 0.091 3278 Dihedral : 6.152 100.559 2674 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2439 helix: -1.50 (0.38), residues: 164 sheet: -0.24 (0.17), residues: 844 loop : -1.95 (0.16), residues: 1431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 267 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 82 residues processed: 357 average time/residue: 1.0919 time to fit residues: 446.8913 Evaluate side-chains 317 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 235 time to evaluate : 2.150 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 82 outliers final: 69 residues processed: 15 average time/residue: 0.2435 time to fit residues: 8.7907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 0.6980 chunk 232 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 161 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 194 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN H 243 HIS H 445 GLN K 316 ASN K 457 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 1.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 18658 Z= 0.240 Angle : 0.882 22.245 25586 Z= 0.420 Chirality : 0.047 0.327 3080 Planarity : 0.005 0.060 3278 Dihedral : 5.869 99.582 2674 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 4.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.72 (0.16), residues: 2439 helix: -1.23 (0.39), residues: 167 sheet: -0.08 (0.18), residues: 831 loop : -1.86 (0.16), residues: 1441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 267 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 70 residues processed: 338 average time/residue: 1.0703 time to fit residues: 414.3152 Evaluate side-chains 311 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 241 time to evaluate : 2.242 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 70 outliers final: 66 residues processed: 7 average time/residue: 0.2928 time to fit residues: 5.8734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 0.5980 chunk 207 optimal weight: 0.0980 chunk 59 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 ASN H 243 HIS H 445 GLN K 316 ASN K 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.118071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.083310 restraints weight = 47626.883| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.61 r_work: 0.3237 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 1.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 18658 Z= 0.239 Angle : 0.878 21.608 25586 Z= 0.415 Chirality : 0.046 0.318 3080 Planarity : 0.005 0.060 3278 Dihedral : 5.760 99.937 2674 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.60 (0.17), residues: 2439 helix: -1.11 (0.40), residues: 173 sheet: 0.01 (0.18), residues: 835 loop : -1.79 (0.16), residues: 1431 =============================================================================== Job complete usr+sys time: 7812.42 seconds wall clock time: 138 minutes 15.31 seconds (8295.31 seconds total)