Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 06:05:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/10_2023/6ue9_20751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/10_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_20751/10_2023/6ue9_20751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/10_2023/6ue9_20751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/10_2023/6ue9_20751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/10_2023/6ue9_20751.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.013 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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 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: 11.34, per 1000 atoms: 0.62 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: 7.56 Conformation dependent library (CDL) restraints added in 2.9 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: 2.11 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: 6.27 Time building geometry restraints manager: 8.01 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=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.41e+00 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=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.67e+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=" 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 angle pdb=" N VAL C 158 " pdb=" CA VAL C 158 " pdb=" C VAL C 158 " ideal model delta sigma weight residual 113.20 108.46 4.74 9.60e-01 1.09e+00 2.43e+01 angle pdb=" CA SER A 260 " pdb=" C SER A 260 " pdb=" N GLU A 261 " ideal model delta sigma weight residual 116.84 125.20 -8.36 1.71e+00 3.42e-01 2.39e+01 ... (remaining 25581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10004 17.96 - 35.93: 893 35.93 - 53.89: 159 53.89 - 71.85: 19 71.85 - 89.81: 9 Dihedral angle restraints: 11084 sinusoidal: 3980 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 11081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2647 0.085 - 0.170: 391 0.170 - 0.254: 32 0.254 - 0.339: 5 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 4.32e+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 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: 0.010 Normalize map: mean=0, sd=1: 8.880 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: 0.000 Extract box with map and model: 16.340 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 50.550 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3798 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= 0.448 Angle : 1.049 16.113 25586 Z= 0.558 Chirality : 0.062 0.424 3080 Planarity : 0.008 0.075 3278 Dihedral : 13.690 86.726 6375 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 % Allowed : 9.85 % Favored : 89.83 % 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 : 1.965 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: 0.9824 time to fit residues: 615.3064 Evaluate side-chains 261 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 2.150 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.2557 time to fit residues: 3.5910 ------------------------------------------------------------------------------- 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 327 HIS 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 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4963 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 18658 Z= 0.310 Angle : 0.950 13.355 25586 Z= 0.451 Chirality : 0.050 0.351 3080 Planarity : 0.007 0.077 3278 Dihedral : 6.274 29.807 2598 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 7.67 % Allowed : 20.13 % Favored : 72.20 % 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: -3.07 (0.15), residues: 2439 helix: -3.34 (0.28), residues: 143 sheet: -0.92 (0.17), residues: 816 loop : -2.70 (0.14), residues: 1480 *********************** 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 492 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 348 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 55 residues processed: 451 average time/residue: 0.8205 time to fit residues: 440.3750 Evaluate side-chains 333 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 278 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 36 residues processed: 19 average time/residue: 0.2645 time to fit residues: 10.6899 ------------------------------------------------------------------------------- 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: 0.9980 chunk 185 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 222 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 chunk 221 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN C 530 GLN F 327 HIS ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 18658 Z= 0.255 Angle : 0.836 13.343 25586 Z= 0.394 Chirality : 0.047 0.363 3080 Planarity : 0.006 0.068 3278 Dihedral : 5.493 33.553 2598 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 8.09 % Allowed : 23.06 % Favored : 68.85 % 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: -2.48 (0.16), residues: 2439 helix: -2.35 (0.35), residues: 148 sheet: -0.48 (0.18), residues: 812 loop : -2.38 (0.14), residues: 1479 *********************** 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 497 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 345 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 66 residues processed: 452 average time/residue: 0.7631 time to fit residues: 414.1437 Evaluate side-chains 342 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 276 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 47 residues processed: 20 average time/residue: 0.2056 time to fit residues: 9.8187 ------------------------------------------------------------------------------- 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: 1.9990 chunk 167 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 106 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 212 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 445 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN E 459 ASN H 243 HIS ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 HIS K 457 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.8342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 18658 Z= 0.320 Angle : 0.910 13.821 25586 Z= 0.433 Chirality : 0.051 0.420 3080 Planarity : 0.006 0.078 3278 Dihedral : 5.552 35.787 2598 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.30 % Favored : 92.66 % Rotamer: Outliers : 9.00 % Allowed : 24.49 % Favored : 66.51 % 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: -2.27 (0.16), residues: 2439 helix: -1.68 (0.39), residues: 151 sheet: -0.46 (0.18), residues: 796 loop : -2.19 (0.15), residues: 1492 *********************** 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 551 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 382 time to evaluate : 2.073 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: 169 outliers final: 87 residues processed: 502 average time/residue: 0.9257 time to fit residues: 542.6167 Evaluate side-chains 395 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 308 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 60 residues processed: 28 average time/residue: 0.2093 time to fit residues: 12.8235 ------------------------------------------------------------------------------- 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: 0.9980 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN C 32 HIS C 40 GLN C 84 GLN C 150 GLN C 284 GLN D 90 ASN F 316 ASN G 350 HIS ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN H 243 HIS H 316 ASN H 436 HIS ** H 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 ASN K 445 GLN K 457 HIS L 249 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 1.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.162 18658 Z= 0.533 Angle : 1.198 26.772 25586 Z= 0.582 Chirality : 0.059 0.596 3080 Planarity : 0.008 0.129 3278 Dihedral : 7.022 36.668 2598 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 10.38 % Allowed : 27.69 % Favored : 61.93 % Cbeta Deviations : 0.00 % 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: -2.72 (0.16), residues: 2439 helix: -2.36 (0.36), residues: 158 sheet: -0.79 (0.18), residues: 805 loop : -2.45 (0.14), residues: 1476 *********************** 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 565 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 370 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 67 residues processed: 517 average time/residue: 1.0149 time to fit residues: 604.4555 Evaluate side-chains 317 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 250 time to evaluate : 2.291 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 60 residues processed: 7 average time/residue: 0.4147 time to fit residues: 6.7863 ------------------------------------------------------------------------------- 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: 0.8980 chunk 213 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 362 ASN D 81 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS F 249 HIS G 350 HIS H 243 HIS ** H 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 1.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18658 Z= 0.255 Angle : 0.922 29.688 25586 Z= 0.427 Chirality : 0.049 0.359 3080 Planarity : 0.005 0.057 3278 Dihedral : 5.879 33.462 2598 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.34 % Allowed : 34.24 % Favored : 59.42 % 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: -2.37 (0.16), residues: 2439 helix: -2.09 (0.37), residues: 164 sheet: -0.58 (0.18), residues: 807 loop : -2.19 (0.15), residues: 1468 *********************** 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 435 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 316 time to evaluate : 2.150 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: 119 outliers final: 73 residues processed: 411 average time/residue: 1.0875 time to fit residues: 510.3953 Evaluate side-chains 339 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 266 time to evaluate : 1.964 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 63 residues processed: 12 average time/residue: 0.3431 time to fit residues: 8.3499 ------------------------------------------------------------------------------- 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: 0.0070 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 236 optimal weight: 0.4980 chunk 147 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS G 445 GLN H 243 HIS ** H 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 1.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18658 Z= 0.229 Angle : 0.866 25.937 25586 Z= 0.401 Chirality : 0.047 0.354 3080 Planarity : 0.005 0.059 3278 Dihedral : 5.275 30.493 2598 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.75 % Allowed : 35.46 % Favored : 58.79 % 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: -2.11 (0.16), residues: 2439 helix: -1.69 (0.38), residues: 166 sheet: -0.33 (0.18), residues: 810 loop : -2.09 (0.15), residues: 1463 *********************** 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 399 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 291 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 70 residues processed: 380 average time/residue: 1.0787 time to fit residues: 469.3747 Evaluate side-chains 330 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 260 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 62 residues processed: 9 average time/residue: 0.3877 time to fit residues: 7.3125 ------------------------------------------------------------------------------- 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: 1.9990 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS ** H 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 1.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18658 Z= 0.387 Angle : 0.973 27.395 25586 Z= 0.462 Chirality : 0.050 0.366 3080 Planarity : 0.006 0.079 3278 Dihedral : 5.683 31.426 2598 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 6.55 % Allowed : 34.29 % Favored : 59.16 % 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: -2.14 (0.16), residues: 2439 helix: -1.52 (0.40), residues: 152 sheet: -0.42 (0.17), residues: 831 loop : -2.12 (0.15), residues: 1456 *********************** 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 379 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 256 time to evaluate : 2.133 Fit side-chains revert: symmetry clash outliers start: 123 outliers final: 72 residues processed: 349 average time/residue: 1.1071 time to fit residues: 443.1880 Evaluate side-chains 301 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 229 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 61 residues processed: 11 average time/residue: 0.3330 time to fit residues: 8.1438 ------------------------------------------------------------------------------- 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: 2.9990 chunk 226 optimal weight: 0.0980 chunk 206 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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** D 45 ASN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS ** H 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 1.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18658 Z= 0.386 Angle : 0.964 27.948 25586 Z= 0.457 Chirality : 0.050 0.354 3080 Planarity : 0.006 0.058 3278 Dihedral : 5.635 31.936 2598 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 5.17 % Allowed : 35.36 % Favored : 59.48 % 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: -2.20 (0.16), residues: 2439 helix: -1.63 (0.38), residues: 154 sheet: -0.55 (0.17), residues: 829 loop : -2.08 (0.15), residues: 1456 *********************** 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 358 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 261 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 68 residues processed: 338 average time/residue: 1.1733 time to fit residues: 449.8702 Evaluate side-chains 297 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 229 time to evaluate : 2.206 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 59 residues processed: 9 average time/residue: 0.3813 time to fit residues: 7.5799 ------------------------------------------------------------------------------- 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: 2.9990 chunk 232 optimal weight: 0.0370 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 244 optimal weight: 0.4980 chunk 224 optimal weight: 0.0070 chunk 194 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 K 316 ASN K 457 HIS ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 1.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18658 Z= 0.248 Angle : 0.942 25.606 25586 Z= 0.438 Chirality : 0.047 0.353 3080 Planarity : 0.005 0.060 3278 Dihedral : 5.220 29.338 2598 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.21 % Allowed : 36.85 % Favored : 58.95 % 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: -1.92 (0.16), residues: 2439 helix: -1.38 (0.38), residues: 155 sheet: -0.38 (0.18), residues: 832 loop : -1.88 (0.16), residues: 1452 ********************** 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 351 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 272 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 68 residues processed: 341 average time/residue: 1.0707 time to fit residues: 418.0557 Evaluate side-chains 304 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 236 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 62 residues processed: 7 average time/residue: 0.2620 time to fit residues: 5.7196 ------------------------------------------------------------------------------- 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: 4.9990 chunk 207 optimal weight: 30.0000 chunk 59 optimal weight: 0.1980 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.0050 chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 445 GLN D 45 ASN G 406 GLN ** G 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS K 445 GLN K 457 HIS ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.117082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.082592 restraints weight = 47689.085| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.49 r_work: 0.3221 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 1.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18658 Z= 0.243 Angle : 0.918 24.540 25586 Z= 0.428 Chirality : 0.047 0.346 3080 Planarity : 0.006 0.077 3278 Dihedral : 4.971 27.480 2598 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.37 % Allowed : 37.01 % Favored : 58.63 % 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: -1.81 (0.16), residues: 2439 helix: -1.40 (0.38), residues: 156 sheet: -0.27 (0.18), residues: 831 loop : -1.82 (0.16), residues: 1452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7801.94 seconds wall clock time: 139 minutes 18.77 seconds (8358.77 seconds total)