Starting phenix.real_space_refine on Sun Apr 7 13:42:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/04_2024/7a5r_11648.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/04_2024/7a5r_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_11648/04_2024/7a5r_11648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/04_2024/7a5r_11648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/04_2024/7a5r_11648.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/04_2024/7a5r_11648.pdb" } resolution = 3.7 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= 0.002 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-dev-5288/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.99, per 1000 atoms: 0.56 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: 3.68 Conformation dependent library (CDL) restraints added in 2.0 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: 1.29 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: 3.15 Time building geometry restraints manager: 4.05 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: 5891 17.87 - 35.75: 497 35.75 - 53.62: 106 53.62 - 71.49: 22 71.49 - 89.37: 6 Dihedral angle restraints: 6522 sinusoidal: 2584 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 6519 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: 2.790 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: 13.080 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.920 Find NCS groups from input model: 0.580 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.680 ------------------------------------------------------------------------------- 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 : 14.013 89.368 3954 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 % Allowed : 6.13 % Favored : 93.19 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 83 HIS 0.002 0.001 HIS L 204 PHE 0.017 0.002 PHE H 29 TYR 0.019 0.002 TYR B 351 ARG 0.005 0.001 ARG A 328 *********************** 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 : 1.298 Fit side-chains REVERT: H 142 LEU cc_start: 0.7623 (pp) cc_final: 0.7406 (pp) REVERT: L 132 LYS cc_start: 0.8278 (mttt) cc_final: 0.8055 (pttm) REVERT: M 51 LYS cc_start: 0.8025 (mttt) cc_final: 0.7779 (tttm) REVERT: M 132 LYS cc_start: 0.7935 (mttt) cc_final: 0.7720 (pttm) REVERT: I 6 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: I 38 ARG cc_start: 0.8999 (ptm-80) cc_final: 0.8687 (ptm-80) REVERT: I 142 LEU cc_start: 0.7429 (pp) cc_final: 0.7228 (pp) outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.3056 time to fit residues: 73.3033 Evaluate side-chains 121 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain I residue 6 GLN 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: 0.9980 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: 1.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10870 Z= 0.248 Angle : 0.679 8.232 14786 Z= 0.350 Chirality : 0.047 0.144 1652 Planarity : 0.005 0.041 1882 Dihedral : 6.221 59.367 1553 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.35 % Allowed : 9.16 % Favored : 88.49 % 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: -1.47 (0.22), residues: 1318 helix: -2.99 (0.79), residues: 40 sheet: 0.57 (0.23), residues: 510 loop : -2.09 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 83 HIS 0.004 0.001 HIS I 204 PHE 0.016 0.002 PHE L 122 TYR 0.014 0.001 TYR I 180 ARG 0.004 0.001 ARG M 60 *********************** 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 141 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: H 142 LEU cc_start: 0.7655 (pp) cc_final: 0.7371 (pp) REVERT: L 132 LYS cc_start: 0.8374 (mttt) cc_final: 0.7914 (pttm) REVERT: A 471 GLU cc_start: 0.4661 (OUTLIER) cc_final: 0.4078 (tp30) REVERT: B 471 GLU cc_start: 0.4478 (OUTLIER) cc_final: 0.4002 (tp30) REVERT: B 489 TYR cc_start: 0.8826 (m-80) cc_final: 0.8605 (m-80) REVERT: M 132 LYS cc_start: 0.8085 (mttt) cc_final: 0.7781 (pttm) REVERT: M 149 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7673 (tm-30) REVERT: I 142 LEU cc_start: 0.7596 (pp) cc_final: 0.7369 (pp) outliers start: 28 outliers final: 15 residues processed: 132 average time/residue: 0.2690 time to fit residues: 49.9173 Evaluate side-chains 123 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 493 GLN I 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10870 Z= 0.188 Angle : 0.602 7.710 14786 Z= 0.307 Chirality : 0.044 0.153 1652 Planarity : 0.004 0.041 1882 Dihedral : 5.553 52.085 1550 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.44 % Allowed : 11.93 % Favored : 85.63 % 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: -1.30 (0.23), residues: 1318 helix: -3.56 (0.60), residues: 52 sheet: 0.55 (0.23), residues: 528 loop : -1.82 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS H 168 PHE 0.013 0.001 PHE I 126 TYR 0.012 0.001 TYR I 180 ARG 0.003 0.000 ARG A 403 *********************** 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 142 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 2 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.5684 (ppp) REVERT: H 142 LEU cc_start: 0.7620 (pp) cc_final: 0.7339 (pp) REVERT: L 132 LYS cc_start: 0.8393 (mttt) cc_final: 0.7983 (pttm) REVERT: A 471 GLU cc_start: 0.4629 (OUTLIER) cc_final: 0.4132 (tp30) REVERT: B 471 GLU cc_start: 0.4540 (OUTLIER) cc_final: 0.4158 (tp30) REVERT: M 114 ARG cc_start: 0.7418 (ptm-80) cc_final: 0.7141 (ptm160) REVERT: M 132 LYS cc_start: 0.8138 (mttt) cc_final: 0.7771 (pttm) REVERT: M 149 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7572 (tm-30) REVERT: I 67 GLN cc_start: 0.8539 (mm-40) cc_final: 0.7518 (mt0) REVERT: I 142 LEU cc_start: 0.7628 (pp) cc_final: 0.7380 (pp) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 0.2573 time to fit residues: 48.0219 Evaluate side-chains 125 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN A 493 GLN B 321 GLN B 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10870 Z= 0.326 Angle : 0.664 7.949 14786 Z= 0.340 Chirality : 0.047 0.155 1652 Planarity : 0.005 0.042 1882 Dihedral : 5.608 49.703 1547 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.19 % Allowed : 13.70 % Favored : 83.11 % 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: -1.42 (0.22), residues: 1318 helix: -3.80 (0.62), residues: 52 sheet: 0.59 (0.23), residues: 524 loop : -1.99 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.004 0.001 HIS H 168 PHE 0.022 0.002 PHE I 126 TYR 0.021 0.002 TYR I 180 ARG 0.003 0.001 ARG A 457 *********************** 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 148 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6222 (ppp) REVERT: H 142 LEU cc_start: 0.7721 (pp) cc_final: 0.7432 (pp) REVERT: L 31 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7197 (t80) REVERT: L 132 LYS cc_start: 0.8401 (mttt) cc_final: 0.7942 (pttm) REVERT: L 149 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 471 GLU cc_start: 0.4869 (OUTLIER) cc_final: 0.4225 (tp30) REVERT: B 471 GLU cc_start: 0.4807 (OUTLIER) cc_final: 0.4259 (tp30) REVERT: M 51 LYS cc_start: 0.8137 (mttt) cc_final: 0.7695 (tttm) REVERT: M 132 LYS cc_start: 0.8292 (mttt) cc_final: 0.7762 (pttm) REVERT: M 149 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7830 (tm-30) REVERT: I 2 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6367 (ppp) REVERT: I 67 GLN cc_start: 0.8660 (mm-40) cc_final: 0.7692 (mt0) REVERT: I 142 LEU cc_start: 0.7770 (pp) cc_final: 0.7507 (pp) outliers start: 38 outliers final: 28 residues processed: 138 average time/residue: 0.2418 time to fit residues: 47.1358 Evaluate side-chains 133 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 116 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN A 422 ASN B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10870 Z= 0.242 Angle : 0.612 8.139 14786 Z= 0.313 Chirality : 0.045 0.235 1652 Planarity : 0.004 0.043 1882 Dihedral : 5.521 49.204 1547 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.45 % Allowed : 14.87 % Favored : 81.68 % 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: -1.38 (0.22), residues: 1318 helix: -4.00 (0.56), residues: 52 sheet: 0.67 (0.23), residues: 522 loop : -1.98 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.003 0.001 HIS H 168 PHE 0.018 0.002 PHE H 126 TYR 0.014 0.001 TYR I 180 ARG 0.002 0.000 ARG M 60 *********************** 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 149 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: H 67 GLN cc_start: 0.8829 (mm110) cc_final: 0.8511 (mm110) REVERT: H 142 LEU cc_start: 0.7730 (pp) cc_final: 0.7484 (pp) REVERT: L 31 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7190 (t80) REVERT: L 114 ARG cc_start: 0.7513 (ptm-80) cc_final: 0.7229 (ptm160) REVERT: L 132 LYS cc_start: 0.8368 (mttt) cc_final: 0.7884 (pttm) REVERT: L 149 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7792 (tm-30) REVERT: L 155 LYS cc_start: 0.7242 (mmmt) cc_final: 0.6705 (mmmt) REVERT: A 471 GLU cc_start: 0.4706 (OUTLIER) cc_final: 0.4190 (tp30) REVERT: B 471 GLU cc_start: 0.4737 (OUTLIER) cc_final: 0.4248 (tp30) REVERT: M 31 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.6479 (t80) REVERT: M 51 LYS cc_start: 0.8075 (mttt) cc_final: 0.7640 (tttm) REVERT: M 114 ARG cc_start: 0.7427 (ptm-80) cc_final: 0.7155 (ptm160) REVERT: M 132 LYS cc_start: 0.8311 (mttt) cc_final: 0.7767 (pttm) REVERT: M 149 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7751 (tm-30) REVERT: I 2 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6283 (ppp) REVERT: I 67 GLN cc_start: 0.8700 (mm-40) cc_final: 0.7773 (mt0) REVERT: I 142 LEU cc_start: 0.7784 (pp) cc_final: 0.7511 (pp) outliers start: 41 outliers final: 26 residues processed: 138 average time/residue: 0.2401 time to fit residues: 47.0033 Evaluate side-chains 132 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.2980 chunk 25 optimal weight: 0.0870 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2636 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= 0.206 Angle : 0.577 7.348 14786 Z= 0.295 Chirality : 0.044 0.145 1652 Planarity : 0.004 0.042 1882 Dihedral : 5.313 49.520 1547 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.87 % Allowed : 14.96 % Favored : 81.18 % 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: -1.24 (0.22), residues: 1318 helix: -4.38 (0.54), residues: 40 sheet: 0.81 (0.23), residues: 514 loop : -1.91 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS I 168 PHE 0.016 0.001 PHE H 126 TYR 0.012 0.001 TYR H 180 ARG 0.002 0.000 ARG B 408 *********************** 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 152 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 106 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6333 (ppp) REVERT: H 67 GLN cc_start: 0.8812 (mm110) cc_final: 0.8493 (mm110) REVERT: H 142 LEU cc_start: 0.7702 (pp) cc_final: 0.7463 (pp) REVERT: L 31 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7179 (t80) REVERT: L 114 ARG cc_start: 0.7470 (ptm-80) cc_final: 0.7145 (ptm160) REVERT: L 132 LYS cc_start: 0.8366 (mttt) cc_final: 0.7879 (pttm) REVERT: L 149 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7740 (tm-30) REVERT: L 155 LYS cc_start: 0.7284 (mmmt) cc_final: 0.6859 (mmmt) REVERT: A 457 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7726 (ttp80) REVERT: A 471 GLU cc_start: 0.4715 (OUTLIER) cc_final: 0.4199 (tp30) REVERT: B 41 LYS cc_start: 0.7689 (tppt) cc_final: 0.6701 (mtmm) REVERT: B 457 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7763 (ttp80) REVERT: B 471 GLU cc_start: 0.4723 (OUTLIER) cc_final: 0.4288 (tp30) REVERT: M 31 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.6415 (t80) REVERT: M 51 LYS cc_start: 0.8075 (mttt) cc_final: 0.7648 (tttm) REVERT: M 132 LYS cc_start: 0.8329 (mttt) cc_final: 0.7775 (pttm) REVERT: M 149 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7647 (tm-30) REVERT: I 2 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6300 (ppp) REVERT: I 67 GLN cc_start: 0.8707 (mm-40) cc_final: 0.7799 (mt0) REVERT: I 142 LEU cc_start: 0.7772 (pp) cc_final: 0.7511 (pp) outliers start: 46 outliers final: 32 residues processed: 142 average time/residue: 0.2479 time to fit residues: 49.0098 Evaluate side-chains 137 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.0970 chunk 94 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN M 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10870 Z= 0.209 Angle : 0.576 7.446 14786 Z= 0.294 Chirality : 0.044 0.148 1652 Planarity : 0.004 0.043 1882 Dihedral : 5.238 49.265 1547 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.45 % Allowed : 15.13 % Favored : 80.42 % 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: -4.31 (0.56), residues: 40 sheet: 0.80 (0.23), residues: 514 loop : -1.84 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS I 204 PHE 0.014 0.001 PHE H 126 TYR 0.013 0.001 TYR I 180 ARG 0.002 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 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 151 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 98 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6403 (ppp) REVERT: H 67 GLN cc_start: 0.8824 (mm110) cc_final: 0.8494 (mm110) REVERT: H 142 LEU cc_start: 0.7797 (pp) cc_final: 0.7556 (pp) REVERT: L 114 ARG cc_start: 0.7433 (ptm-80) cc_final: 0.7116 (ptm160) REVERT: L 132 LYS cc_start: 0.8379 (mttt) cc_final: 0.7854 (pttm) REVERT: L 149 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7740 (tm-30) REVERT: L 155 LYS cc_start: 0.7160 (mmmt) cc_final: 0.6777 (mmmt) REVERT: A 457 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7779 (ttp80) REVERT: A 471 GLU cc_start: 0.4681 (OUTLIER) cc_final: 0.4238 (tp30) REVERT: B 457 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7773 (ttp80) REVERT: B 471 GLU cc_start: 0.4644 (OUTLIER) cc_final: 0.4220 (tp30) REVERT: M 31 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6301 (t80) REVERT: M 51 LYS cc_start: 0.8122 (mttt) cc_final: 0.7637 (tttm) REVERT: M 132 LYS cc_start: 0.8359 (mttt) cc_final: 0.7732 (pttm) REVERT: M 149 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7686 (tm-30) REVERT: M 155 LYS cc_start: 0.7126 (mmmt) cc_final: 0.6683 (mmmt) REVERT: I 2 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6417 (ppp) REVERT: I 67 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7795 (mt0) REVERT: I 142 LEU cc_start: 0.7787 (pp) cc_final: 0.7525 (pp) outliers start: 53 outliers final: 36 residues processed: 142 average time/residue: 0.2438 time to fit residues: 48.5701 Evaluate side-chains 139 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 96 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2918 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= 0.195 Angle : 0.562 7.139 14786 Z= 0.286 Chirality : 0.044 0.147 1652 Planarity : 0.004 0.043 1882 Dihedral : 5.154 49.403 1547 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.03 % Allowed : 15.71 % Favored : 80.25 % 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: -1.15 (0.22), residues: 1318 helix: -4.39 (0.54), residues: 40 sheet: 0.80 (0.23), residues: 514 loop : -1.79 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS H 168 PHE 0.013 0.001 PHE H 126 TYR 0.011 0.001 TYR L 55 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 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 148 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 100 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6473 (ppp) REVERT: H 67 GLN cc_start: 0.8803 (mm110) cc_final: 0.8462 (mm110) REVERT: H 142 LEU cc_start: 0.7820 (pp) cc_final: 0.7581 (pp) REVERT: L 31 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.6926 (t80) REVERT: L 114 ARG cc_start: 0.7385 (ptm-80) cc_final: 0.7066 (ptm160) REVERT: L 132 LYS cc_start: 0.8339 (mttt) cc_final: 0.7803 (pttm) REVERT: L 149 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7741 (tm-30) REVERT: L 155 LYS cc_start: 0.7149 (mmmt) cc_final: 0.6806 (mmmt) REVERT: A 457 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7801 (ttp80) REVERT: A 471 GLU cc_start: 0.4744 (OUTLIER) cc_final: 0.4252 (tp30) REVERT: B 457 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7789 (ttp80) REVERT: B 471 GLU cc_start: 0.4630 (OUTLIER) cc_final: 0.4213 (tp30) REVERT: M 31 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.6208 (t80) REVERT: M 51 LYS cc_start: 0.8117 (mttt) cc_final: 0.7633 (tttm) REVERT: M 132 LYS cc_start: 0.8391 (mttt) cc_final: 0.7726 (pttm) REVERT: M 149 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7652 (tm-30) REVERT: M 155 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6705 (mmmt) REVERT: I 2 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.6545 (ppp) REVERT: I 67 GLN cc_start: 0.8650 (mm-40) cc_final: 0.7767 (mt0) REVERT: I 142 LEU cc_start: 0.7853 (pp) cc_final: 0.7617 (pp) outliers start: 48 outliers final: 38 residues processed: 138 average time/residue: 0.2402 time to fit residues: 46.4740 Evaluate side-chains 145 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 99 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 0.0970 chunk 72 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10870 Z= 0.158 Angle : 0.538 6.810 14786 Z= 0.273 Chirality : 0.043 0.148 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.967 49.905 1547 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.70 % Allowed : 16.39 % Favored : 79.92 % 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: -1.04 (0.22), residues: 1318 helix: -4.39 (0.52), residues: 40 sheet: 0.85 (0.23), residues: 514 loop : -1.68 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS M 204 PHE 0.009 0.001 PHE H 126 TYR 0.011 0.001 TYR L 55 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 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 150 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 106 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.6448 (ppp) REVERT: H 16 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7107 (mt-10) REVERT: H 142 LEU cc_start: 0.7792 (pp) cc_final: 0.7556 (pp) REVERT: L 31 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.6886 (t80) REVERT: L 132 LYS cc_start: 0.8328 (mttt) cc_final: 0.7798 (pttm) REVERT: L 149 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7701 (tm-30) REVERT: L 155 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6805 (mmmt) REVERT: A 457 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7735 (ttp80) REVERT: A 471 GLU cc_start: 0.4679 (OUTLIER) cc_final: 0.4233 (tp30) REVERT: B 471 GLU cc_start: 0.4652 (OUTLIER) cc_final: 0.4185 (tp30) REVERT: M 31 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.6228 (t80) REVERT: M 132 LYS cc_start: 0.8400 (mttt) cc_final: 0.7719 (pttm) REVERT: M 149 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7608 (tm-30) REVERT: M 155 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6752 (mmmt) REVERT: I 2 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.6527 (ppp) REVERT: I 67 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7719 (mt0) REVERT: I 133 LYS cc_start: 0.7100 (mttt) cc_final: 0.6634 (pttp) REVERT: I 142 LEU cc_start: 0.7860 (pp) cc_final: 0.7623 (pp) outliers start: 44 outliers final: 34 residues processed: 141 average time/residue: 0.2407 time to fit residues: 47.7403 Evaluate side-chains 145 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 6 GLN M 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10870 Z= 0.374 Angle : 0.672 8.181 14786 Z= 0.345 Chirality : 0.047 0.160 1652 Planarity : 0.005 0.047 1882 Dihedral : 5.607 50.025 1547 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.70 % Allowed : 16.30 % Favored : 80.00 % 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: -1.32 (0.22), residues: 1318 helix: -4.57 (0.48), residues: 40 sheet: 0.68 (0.23), residues: 516 loop : -1.90 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 353 HIS 0.004 0.001 HIS H 204 PHE 0.027 0.002 PHE H 126 TYR 0.021 0.002 TYR H 180 ARG 0.003 0.001 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 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 151 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 107 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.6620 (ppp) REVERT: H 67 GLN cc_start: 0.8807 (mm110) cc_final: 0.8481 (mm110) REVERT: H 142 LEU cc_start: 0.7928 (pp) cc_final: 0.7682 (pp) REVERT: L 31 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.6495 (t80) REVERT: L 132 LYS cc_start: 0.8367 (mttt) cc_final: 0.7780 (pttm) REVERT: L 149 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7958 (tm-30) REVERT: L 155 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6940 (mmmt) REVERT: A 41 LYS cc_start: 0.7840 (tppt) cc_final: 0.6939 (mtmm) REVERT: A 457 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7811 (ttp80) REVERT: A 471 GLU cc_start: 0.4865 (OUTLIER) cc_final: 0.4299 (tp30) REVERT: B 471 GLU cc_start: 0.4821 (OUTLIER) cc_final: 0.4269 (tp30) REVERT: M 31 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.6214 (t80) REVERT: M 51 LYS cc_start: 0.8248 (mttt) cc_final: 0.7705 (tttm) REVERT: M 132 LYS cc_start: 0.8421 (mttt) cc_final: 0.7760 (pttm) REVERT: M 149 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7908 (tm-30) REVERT: M 155 LYS cc_start: 0.7266 (mmmt) cc_final: 0.6828 (mmmt) REVERT: I 2 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6720 (ppp) REVERT: I 67 GLN cc_start: 0.8636 (mm-40) cc_final: 0.7698 (mt0) REVERT: I 142 LEU cc_start: 0.7851 (pp) cc_final: 0.7566 (pp) outliers start: 44 outliers final: 34 residues processed: 145 average time/residue: 0.2625 time to fit residues: 53.5728 Evaluate side-chains 141 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 100 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 44 optimal weight: 0.0570 chunk 109 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN M 6 GLN M 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122156 restraints weight = 16405.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123932 restraints weight = 12348.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125097 restraints weight = 10049.780| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10870 Z= 0.177 Angle : 0.570 7.951 14786 Z= 0.288 Chirality : 0.044 0.144 1652 Planarity : 0.004 0.043 1882 Dihedral : 5.274 49.400 1547 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.36 % Allowed : 16.89 % Favored : 79.75 % 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: -1.14 (0.22), residues: 1318 helix: -4.53 (0.48), residues: 40 sheet: 0.85 (0.23), residues: 510 loop : -1.78 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS M 204 PHE 0.010 0.001 PHE H 170 TYR 0.011 0.001 TYR L 55 ARG 0.003 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.32 seconds wall clock time: 42 minutes 11.14 seconds (2531.14 seconds total)