Starting phenix.real_space_refine (version: 1.21rc1) on Thu May 4 23:54:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/05_2023/7a5r_11648.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/05_2023/7a5r_11648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/05_2023/7a5r_11648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/05_2023/7a5r_11648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/05_2023/7a5r_11648.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/05_2023/7a5r_11648.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.038 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 40 5.16 5 C 6760 2.51 5 N 1748 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 16": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 148": "OD1" <-> "OD2" Residue "H PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 152": "OE1" <-> "OE2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 212": "OD1" <-> "OD2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ASP 9": "OD1" <-> "OD2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 76": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "L TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "L ASP 176": "OD1" <-> "OD2" Residue "L TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M ASP 9": "OD1" <-> "OD2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ASP 66": "OD1" <-> "OD2" Residue "M PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M ASP 88": "OD1" <-> "OD2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 129": "OE1" <-> "OE2" Residue "M TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M ASP 176": "OD1" <-> "OD2" Residue "M TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 16": "OE1" <-> "OE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 55": "OD1" <-> "OD2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 148": "OD1" <-> "OD2" Residue "I PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "I TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "I GLU 216": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 10608 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1595 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "L" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 190} Chain breaks: 2 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2113 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 17, 'TRANS': 246} Chain breaks: 4 Chain: "B" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2113 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 17, 'TRANS': 246} Chain breaks: 4 Chain: "M" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 190} Chain breaks: 2 Chain: "I" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1595 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "C" 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: "D" 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 Time building chain proxies: 6.08, per 1000 atoms: 0.57 Number of scatterers: 10608 At special positions: 0 Unit cell: (138.049, 166.311, 71.742, 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 40 16.00 O 2060 8.00 N 1748 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.04 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 343 " " NAG D 1 " - " ASN B 343 " Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 1.5 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 30 sheets defined 6.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.689A pdb=" N LEU L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 134' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.238A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.758A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 134 removed outlier: 3.690A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 127 through 134' Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.342A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 144 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 148 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.772A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER L 120 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN L 143 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AB4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU M 11 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.773A pdb=" N LYS M 36 " --> pdb=" O TYR M 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER M 120 " --> pdb=" O ASN M 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN M 143 " --> pdb=" O SER M 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR M 198 " --> pdb=" O PHE M 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL I 108 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 128 removed outlier: 4.343A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 144 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 184 " --> pdb=" O CYS I 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 148 " --> pdb=" O TYR I 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 792 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: 3.04 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3324 1.34 - 1.46: 2768 1.46 - 1.58: 4730 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 10870 Sorted by residual: bond pdb=" N LEU H 174 " pdb=" CA LEU H 174 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.14e+00 bond pdb=" N LEU I 174 " pdb=" CA LEU I 174 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.44e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 10865 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 388 106.60 - 113.45: 5794 113.45 - 120.30: 3770 120.30 - 127.15: 4704 127.15 - 134.00: 130 Bond angle restraints: 14786 Sorted by residual: angle pdb=" C ASN B 370 " pdb=" CA ASN B 370 " pdb=" CB ASN B 370 " ideal model delta sigma weight residual 111.91 116.08 -4.17 1.52e+00 4.33e-01 7.53e+00 angle pdb=" CA ILE M 2 " pdb=" CB ILE M 2 " pdb=" CG1 ILE M 2 " ideal model delta sigma weight residual 110.40 115.06 -4.66 1.70e+00 3.46e-01 7.51e+00 angle pdb=" CA ILE L 2 " pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.45e+00 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 111.91 116.05 -4.14 1.52e+00 4.33e-01 7.42e+00 angle pdb=" C TYR M 146 " pdb=" N PRO M 147 " pdb=" CA PRO M 147 " ideal model delta sigma weight residual 127.00 133.25 -6.25 2.40e+00 1.74e-01 6.78e+00 ... (remaining 14781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5815 17.87 - 35.75: 497 35.75 - 53.62: 98 53.62 - 71.49: 22 71.49 - 89.37: 6 Dihedral angle restraints: 6438 sinusoidal: 2500 harmonic: 3938 Sorted by residual: dihedral pdb=" CB CYS H 144 " pdb=" SG CYS H 144 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 129.54 -36.54 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS I 144 " pdb=" SG CYS I 144 " pdb=" SG CYS I 200 " pdb=" CB CYS I 200 " ideal model delta sinusoidal sigma weight residual 93.00 129.53 -36.53 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -122.12 36.12 1 1.00e+01 1.00e-02 1.85e+01 ... (remaining 6435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 964 0.035 - 0.069: 406 0.069 - 0.104: 190 0.104 - 0.138: 83 0.138 - 0.173: 9 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB ILE L 34 " pdb=" CA ILE L 34 " pdb=" CG1 ILE L 34 " pdb=" CG2 ILE L 34 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CB ILE M 34 " pdb=" CA ILE M 34 " pdb=" CG1 ILE M 34 " pdb=" CG2 ILE M 34 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR I 91 " pdb=" CA THR I 91 " pdb=" OG1 THR I 91 " pdb=" CG2 THR I 91 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1649 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO H 153 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 152 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO I 153 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO I 153 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 153 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 512 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C VAL B 512 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL B 512 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 513 " -0.010 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1233 2.75 - 3.29: 9288 3.29 - 3.83: 15432 3.83 - 4.36: 17584 4.36 - 4.90: 32591 Nonbonded interactions: 76128 Sorted by model distance: nonbonded pdb=" OG SER M 127 " pdb=" NZ LYS I 218 " model vdw 2.218 2.520 nonbonded pdb=" OG SER M 120 " pdb=" OD1 ASN M 143 " model vdw 2.381 2.440 nonbonded pdb=" OG SER L 120 " pdb=" OD1 ASN L 143 " model vdw 2.381 2.440 nonbonded pdb=" NZ LYS H 218 " pdb=" OG SER L 127 " model vdw 2.405 2.520 nonbonded pdb=" O LEU H 174 " pdb=" CD1 LEU H 174 " model vdw 2.418 3.460 ... (remaining 76123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 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: 0.010 Extract box with map and model: 13.390 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.950 Find NCS groups from input model: 0.570 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.004 0.038 10870 Z= 0.266 Angle : 0.809 8.411 14786 Z= 0.437 Chirality : 0.050 0.173 1652 Planarity : 0.005 0.051 1882 Dihedral : 13.987 89.368 3870 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.59 % Favored : 92.26 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.97 (0.22), residues: 1318 helix: -2.70 (0.69), residues: 52 sheet: 0.16 (0.24), residues: 482 loop : -2.31 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 1.188 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.2911 time to fit residues: 69.4471 Evaluate side-chains 118 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0897 time to fit residues: 2.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 77 ASN L 44 GLN L 106 GLN A 49 HIS A 271 GLN A 321 GLN B 271 GLN M 44 GLN M 106 GLN I 39 GLN I 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 10870 Z= 0.240 Angle : 0.677 8.113 14786 Z= 0.347 Chirality : 0.047 0.149 1652 Planarity : 0.005 0.040 1882 Dihedral : 4.748 19.048 1462 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.39 (0.22), residues: 1318 helix: -3.42 (0.80), residues: 28 sheet: 0.58 (0.23), residues: 510 loop : -2.00 (0.20), residues: 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 132 average time/residue: 0.2538 time to fit residues: 46.7531 Evaluate side-chains 122 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0962 time to fit residues: 4.1984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10870 Z= 0.209 Angle : 0.610 7.833 14786 Z= 0.312 Chirality : 0.045 0.150 1652 Planarity : 0.004 0.041 1882 Dihedral : 4.542 18.570 1462 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.26 (0.23), residues: 1318 helix: -3.95 (0.60), residues: 40 sheet: 0.60 (0.24), residues: 514 loop : -1.78 (0.21), residues: 764 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 0.2466 time to fit residues: 43.5918 Evaluate side-chains 116 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0965 time to fit residues: 3.6677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 493 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10870 Z= 0.226 Angle : 0.611 7.685 14786 Z= 0.309 Chirality : 0.045 0.157 1652 Planarity : 0.004 0.041 1882 Dihedral : 4.628 20.045 1462 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.19 (0.22), residues: 1318 helix: -4.09 (0.62), residues: 40 sheet: 0.76 (0.23), residues: 516 loop : -1.84 (0.20), residues: 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.267 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 118 average time/residue: 0.2540 time to fit residues: 42.0361 Evaluate side-chains 106 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0995 time to fit residues: 3.0052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 110 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.0000 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10870 Z= 0.189 Angle : 0.603 11.380 14786 Z= 0.303 Chirality : 0.044 0.145 1652 Planarity : 0.004 0.041 1882 Dihedral : 4.619 22.996 1462 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.20 (0.22), residues: 1318 helix: -4.21 (0.58), residues: 40 sheet: 0.86 (0.23), residues: 514 loop : -1.91 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.253 Fit side-chains outliers start: 22 outliers final: 5 residues processed: 125 average time/residue: 0.2332 time to fit residues: 41.7136 Evaluate side-chains 108 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0888 time to fit residues: 2.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 68 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN M 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 10870 Z= 0.161 Angle : 0.567 7.389 14786 Z= 0.286 Chirality : 0.043 0.179 1652 Planarity : 0.004 0.041 1882 Dihedral : 4.385 21.452 1462 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.05 (0.22), residues: 1318 helix: -4.32 (0.51), residues: 40 sheet: 0.88 (0.23), residues: 514 loop : -1.73 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.158 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 112 average time/residue: 0.2321 time to fit residues: 37.5489 Evaluate side-chains 105 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1422 time to fit residues: 3.2593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5243 > 50: distance: 37 - 42: 12.714 distance: 42 - 43: 13.316 distance: 43 - 44: 17.416 distance: 44 - 45: 6.719 distance: 44 - 46: 30.752 distance: 46 - 47: 14.593 distance: 47 - 48: 15.218 distance: 47 - 50: 9.502 distance: 48 - 49: 17.510 distance: 48 - 55: 12.239 distance: 50 - 51: 27.132 distance: 51 - 52: 28.722 distance: 52 - 53: 24.725 distance: 52 - 54: 19.992 distance: 55 - 56: 7.369 distance: 56 - 57: 4.031 distance: 56 - 59: 12.053 distance: 57 - 58: 13.385 distance: 57 - 62: 4.429 distance: 59 - 60: 8.074 distance: 59 - 61: 13.111 distance: 62 - 63: 4.874 distance: 63 - 64: 14.005 distance: 64 - 65: 22.686 distance: 64 - 66: 32.601 distance: 66 - 67: 7.736 distance: 67 - 68: 6.371 distance: 67 - 70: 24.357 distance: 68 - 69: 11.489 distance: 68 - 75: 11.595 distance: 69 - 96: 16.344 distance: 70 - 71: 7.472 distance: 71 - 72: 20.423 distance: 72 - 73: 12.681 distance: 73 - 74: 13.568 distance: 75 - 76: 13.538 distance: 76 - 77: 13.666 distance: 76 - 79: 12.686 distance: 77 - 78: 12.395 distance: 77 - 83: 17.367 distance: 78 - 108: 34.540 distance: 79 - 80: 15.628 distance: 79 - 81: 10.033 distance: 80 - 82: 12.939 distance: 83 - 84: 25.405 distance: 84 - 85: 25.737 distance: 84 - 87: 28.833 distance: 85 - 86: 9.077 distance: 85 - 88: 29.424 distance: 88 - 89: 14.412 distance: 89 - 90: 7.821 distance: 89 - 92: 24.111 distance: 90 - 91: 18.545 distance: 90 - 96: 8.430 distance: 92 - 93: 17.413 distance: 93 - 94: 21.292 distance: 93 - 95: 22.311 distance: 96 - 97: 29.037 distance: 97 - 98: 21.697 distance: 97 - 100: 14.102 distance: 98 - 99: 19.547 distance: 98 - 108: 23.091 distance: 100 - 101: 13.006 distance: 101 - 102: 23.517 distance: 101 - 103: 22.639 distance: 102 - 104: 9.556 distance: 103 - 105: 19.388 distance: 104 - 106: 6.648 distance: 105 - 106: 11.199 distance: 106 - 107: 3.722 distance: 108 - 109: 20.637 distance: 109 - 110: 9.922 distance: 109 - 112: 22.122 distance: 110 - 111: 12.580 distance: 110 - 116: 10.902 distance: 112 - 113: 21.428 distance: 113 - 114: 25.637 distance: 113 - 115: 14.404