Starting phenix.real_space_refine on Wed Mar 20 05:04:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5c_6706/03_2024/5x5c_6706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5c_6706/03_2024/5x5c_6706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5c_6706/03_2024/5x5c_6706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5c_6706/03_2024/5x5c_6706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5c_6706/03_2024/5x5c_6706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5c_6706/03_2024/5x5c_6706.pdb" } resolution = 4.1 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 153 5.16 5 C 16797 2.51 5 N 4371 2.21 5 O 5097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C ASP 1053": "OD1" <-> "OD2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26418 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8994 Chain: "B" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 41, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1049} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 41, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1049} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "C" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER A 51 " occ=0.54 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 24.68, per 1000 atoms: 0.93 Number of scatterers: 26418 At special positions: 0 Unit cell: (152.1, 163.8, 180.7, 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 153 16.00 O 5097 8.00 N 4371 7.00 C 16797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.05 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.71 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.01 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.06 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.05 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.46 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.56 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.01 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.74 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.02 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.01 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.80 Conformation dependent library (CDL) restraints added in 9.0 seconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 23.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.677A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 341 through 350 removed outlier: 4.206A pdb=" N SER A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.195A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.973A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1018 through 1041 Processing helix chain 'A' and resid 1062 through 1107 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.677A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 390' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.470A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 removed outlier: 3.973A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1011 Processing helix chain 'B' and resid 1018 through 1041 Processing helix chain 'B' and resid 1062 through 1107 Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.677A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.883A pdb=" N SER C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 390' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS C 828 " --> pdb=" O TYR C 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.471A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.972A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1011 Processing helix chain 'C' and resid 1018 through 1041 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.060A pdb=" N ALA C1065 " --> pdb=" O LEU C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.250A pdb=" N ASP A 34 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 4.072A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA A 282 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.788A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE A 782 " --> pdb=" O ILE A1147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 1122 through 1124 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.070A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.548A pdb=" N ALA B 282 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.161A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.510A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 400 through 405 removed outlier: 3.894A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AD1, first strand: chain 'B' and resid 514 through 515 removed outlier: 3.697A pdb=" N VAL B 514 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 505 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AD3, first strand: chain 'B' and resid 779 through 782 removed outlier: 3.563A pdb=" N ILE B 782 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 803 through 804 Processing sheet with id=AD5, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AD6, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.250A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.098A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.510A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AE5, first strand: chain 'C' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.788A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AE8, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 618 through 619 Processing sheet with id=AF1, first strand: chain 'C' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE C 782 " --> pdb=" O ILE C1147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 803 through 804 Processing sheet with id=AF3, first strand: chain 'C' and resid 1122 through 1124 834 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.61 Time building geometry restraints manager: 11.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.53: 22865 1.53 - 1.86: 4156 1.86 - 2.20: 0 2.20 - 2.54: 0 2.54 - 2.88: 1 Bond restraints: 27022 Sorted by residual: bond pdb=" C LEU A 588 " pdb=" N LYS A 595 " ideal model delta sigma weight residual 1.332 2.879 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C TYR B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.333 1.408 -0.075 1.17e-02 7.31e+03 4.12e+01 bond pdb=" C TYR A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.333 1.408 -0.075 1.17e-02 7.31e+03 4.12e+01 bond pdb=" C TYR C 58 " pdb=" N PRO C 59 " ideal model delta sigma weight residual 1.333 1.408 -0.075 1.17e-02 7.31e+03 4.10e+01 bond pdb=" C GLN A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.332 1.406 -0.074 1.30e-02 5.92e+03 3.27e+01 ... (remaining 27017 not shown) Histogram of bond angle deviations from ideal: 27.60 - 50.47: 1 50.47 - 73.33: 0 73.33 - 96.20: 1 96.20 - 119.06: 21694 119.06 - 141.92: 15051 Bond angle restraints: 36747 Sorted by residual: angle pdb=" O LEU A 588 " pdb=" C LEU A 588 " pdb=" N LYS A 595 " ideal model delta sigma weight residual 122.59 27.60 94.99 1.33e+00 5.65e-01 5.10e+03 angle pdb=" N SER B 508 " pdb=" CA SER B 508 " pdb=" C SER B 508 " ideal model delta sigma weight residual 110.35 94.93 15.42 1.36e+00 5.41e-01 1.29e+02 angle pdb=" N TYR B 663 " pdb=" CA TYR B 663 " pdb=" C TYR B 663 " ideal model delta sigma weight residual 111.14 123.25 -12.11 1.08e+00 8.57e-01 1.26e+02 angle pdb=" C SER A1151 " pdb=" N ALA A1152 " pdb=" CA ALA A1152 " ideal model delta sigma weight residual 121.70 140.12 -18.42 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C SER C1151 " pdb=" N ALA C1152 " pdb=" CA ALA C1152 " ideal model delta sigma weight residual 121.70 140.09 -18.39 1.80e+00 3.09e-01 1.04e+02 ... (remaining 36742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 15407 26.90 - 53.80: 580 53.80 - 80.69: 70 80.69 - 107.59: 9 107.59 - 134.49: 9 Dihedral angle restraints: 16075 sinusoidal: 6084 harmonic: 9991 Sorted by residual: dihedral pdb=" CA SER A 856 " pdb=" C SER A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual -180.00 -45.51 -134.49 0 5.00e+00 4.00e-02 7.23e+02 dihedral pdb=" CA SER B 856 " pdb=" C SER B 856 " pdb=" N GLN B 857 " pdb=" CA GLN B 857 " ideal model delta harmonic sigma weight residual -180.00 -45.59 -134.41 0 5.00e+00 4.00e-02 7.23e+02 dihedral pdb=" CA SER C 856 " pdb=" C SER C 856 " pdb=" N GLN C 857 " pdb=" CA GLN C 857 " ideal model delta harmonic sigma weight residual -180.00 -45.64 -134.36 0 5.00e+00 4.00e-02 7.22e+02 ... (remaining 16072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3413 0.097 - 0.195: 599 0.195 - 0.292: 79 0.292 - 0.390: 29 0.390 - 0.487: 11 Chirality restraints: 4131 Sorted by residual: chirality pdb=" CA ASP B 580 " pdb=" N ASP B 580 " pdb=" C ASP B 580 " pdb=" CB ASP B 580 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA ARG C1057 " pdb=" N ARG C1057 " pdb=" C ARG C1057 " pdb=" CB ARG C1057 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA TYR B 663 " pdb=" N TYR B 663 " pdb=" C TYR B 663 " pdb=" CB TYR B 663 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 4128 not shown) Planarity restraints: 4750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 588 " -0.019 2.00e-02 2.50e+03 2.30e-01 5.29e+02 pdb=" C LEU A 588 " 0.253 2.00e-02 2.50e+03 pdb=" O LEU A 588 " -0.362 2.00e-02 2.50e+03 pdb=" N LYS A 595 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 280 " -0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" CD GLN C 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN C 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN C 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 280 " -0.025 2.00e-02 2.50e+03 5.23e-02 2.73e+01 pdb=" CD GLN B 280 " 0.090 2.00e-02 2.50e+03 pdb=" OE1 GLN B 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN B 280 " -0.032 2.00e-02 2.50e+03 ... (remaining 4747 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 79 2.13 - 2.82: 8607 2.82 - 3.51: 35872 3.51 - 4.21: 66253 4.21 - 4.90: 109334 Nonbonded interactions: 220145 Sorted by model distance: nonbonded pdb=" ND2 ASN B 521 " pdb=" CB ALA C 260 " model vdw 1.435 3.540 nonbonded pdb=" OH TYR C 58 " pdb=" O GLY C 331 " model vdw 1.466 2.440 nonbonded pdb=" OH TYR B 58 " pdb=" O GLY B 331 " model vdw 1.466 2.440 nonbonded pdb=" OH TYR A 58 " pdb=" O GLY A 331 " model vdw 1.466 2.440 nonbonded pdb=" N GLN C 78 " pdb=" OD2 ASP C 338 " model vdw 1.474 2.520 ... (remaining 220140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 50 or resid 52 through 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 1206)) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.850 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 85.040 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 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 : 0.014 1.546 27022 Z= 0.769 Angle : 1.753 94.986 36747 Z= 1.029 Chirality : 0.082 0.487 4131 Planarity : 0.009 0.230 4750 Dihedral : 14.644 134.489 9583 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 30.55 Ramachandran Plot: Outliers : 1.21 % Allowed : 13.22 % Favored : 85.57 % Rotamer: Outliers : 5.82 % Allowed : 7.30 % Favored : 86.88 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.22 % Twisted Proline : 0.00 % Twisted General : 1.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.12), residues: 3390 helix: -2.83 (0.14), residues: 674 sheet: -1.27 (0.21), residues: 579 loop : -2.95 (0.11), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP A 960 HIS 0.016 0.004 HIS C1138 PHE 0.038 0.004 PHE A1172 TYR 0.046 0.004 TYR C1171 ARG 0.012 0.002 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 681 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.5280 (t80) REVERT: A 564 THR cc_start: 0.2204 (OUTLIER) cc_final: 0.1842 (p) REVERT: A 604 VAL cc_start: 0.5328 (t) cc_final: 0.5075 (m) REVERT: A 607 SER cc_start: 0.8225 (t) cc_final: 0.7980 (p) REVERT: A 757 MET cc_start: 0.8361 (tpt) cc_final: 0.8124 (mmt) REVERT: A 848 ASN cc_start: 0.8753 (t160) cc_final: 0.8551 (m-40) REVERT: A 895 PHE cc_start: 0.8873 (m-80) cc_final: 0.8345 (m-80) REVERT: A 943 MET cc_start: 0.7159 (ttp) cc_final: 0.6751 (ttp) REVERT: A 947 TYR cc_start: 0.8308 (m-80) cc_final: 0.7835 (m-80) REVERT: B 352 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: B 465 SER cc_start: 0.4707 (OUTLIER) cc_final: 0.4153 (t) REVERT: B 493 LYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3938 (mptt) REVERT: B 511 ARG cc_start: 0.0923 (OUTLIER) cc_final: 0.0217 (mtp180) REVERT: B 563 MET cc_start: 0.3867 (tpp) cc_final: 0.3395 (ttp) REVERT: B 565 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.5005 (tp30) REVERT: B 725 GLU cc_start: 0.7518 (tp30) cc_final: 0.7144 (tm-30) REVERT: B 768 ILE cc_start: 0.8168 (tt) cc_final: 0.7947 (mt) REVERT: B 779 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7801 (mtpp) REVERT: B 799 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9006 (tt) REVERT: B 842 GLN cc_start: 0.9303 (tt0) cc_final: 0.8362 (tm-30) REVERT: B 868 ASP cc_start: 0.8092 (m-30) cc_final: 0.7888 (p0) REVERT: B 893 LEU cc_start: 0.8908 (mt) cc_final: 0.8658 (mt) REVERT: B 913 MET cc_start: 0.8170 (tpt) cc_final: 0.7970 (ttt) REVERT: B 938 LEU cc_start: 0.8586 (tt) cc_final: 0.7904 (mt) REVERT: B 942 ASN cc_start: 0.8566 (m-40) cc_final: 0.8116 (t0) REVERT: B 988 GLN cc_start: 0.8505 (mt0) cc_final: 0.7973 (mt0) REVERT: B 1015 THR cc_start: 0.7730 (p) cc_final: 0.7384 (p) REVERT: B 1094 LEU cc_start: 0.9477 (mt) cc_final: 0.9179 (tp) REVERT: C 50 VAL cc_start: 0.6633 (m) cc_final: 0.6269 (m) REVERT: C 58 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.5959 (t80) REVERT: C 296 ILE cc_start: 0.7207 (mt) cc_final: 0.6960 (mm) REVERT: C 352 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: C 696 MET cc_start: 0.6603 (mmm) cc_final: 0.5555 (tpt) REVERT: C 697 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5441 (tp) REVERT: C 722 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6988 (pt) REVERT: C 794 TYR cc_start: 0.7733 (t80) cc_final: 0.7442 (t80) REVERT: C 815 GLN cc_start: 0.8532 (mt0) cc_final: 0.8164 (tm-30) REVERT: C 827 PHE cc_start: 0.8274 (m-80) cc_final: 0.7925 (m-10) REVERT: C 831 ILE cc_start: 0.8932 (mm) cc_final: 0.8507 (mm) REVERT: C 913 MET cc_start: 0.8009 (tpt) cc_final: 0.7627 (tmm) REVERT: C 1082 VAL cc_start: 0.9603 (t) cc_final: 0.9371 (p) REVERT: C 1089 SER cc_start: 0.9141 (t) cc_final: 0.8594 (p) outliers start: 170 outliers final: 41 residues processed: 830 average time/residue: 0.3704 time to fit residues: 481.0582 Evaluate side-chains 402 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 349 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 268 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 30.0000 chunk 199 optimal weight: 8.9990 chunk 310 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS A 599 GLN A 719 ASN A 800 GLN A 812 ASN A 839 ASN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN A1056 GLN A1084 GLN A1104 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS B 348 HIS ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN B 812 ASN B 839 ASN B 842 GLN B1023 GLN B1066 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN C 167 HIS C 348 HIS C 599 GLN C 792 GLN C 812 ASN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN C1084 GLN ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 27022 Z= 0.345 Angle : 1.064 15.005 36747 Z= 0.552 Chirality : 0.057 0.309 4131 Planarity : 0.008 0.131 4750 Dihedral : 8.564 58.195 3712 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.47 % Favored : 87.11 % Rotamer: Outliers : 0.24 % Allowed : 3.05 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.00 % Twisted General : 1.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.13), residues: 3392 helix: -1.41 (0.17), residues: 676 sheet: -0.55 (0.22), residues: 589 loop : -2.82 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 310 HIS 0.007 0.001 HIS B 348 PHE 0.052 0.003 PHE C 341 TYR 0.045 0.003 TYR B1186 ARG 0.019 0.001 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 461 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 351 TYR cc_start: 0.6833 (m-10) cc_final: 0.6256 (m-10) REVERT: A 682 ILE cc_start: 0.7658 (pt) cc_final: 0.7258 (tp) REVERT: A 757 MET cc_start: 0.8514 (tpt) cc_final: 0.8134 (mmt) REVERT: A 820 LEU cc_start: 0.8657 (mt) cc_final: 0.8319 (mt) REVERT: A 894 LEU cc_start: 0.9049 (pp) cc_final: 0.8824 (pp) REVERT: A 895 PHE cc_start: 0.8834 (m-80) cc_final: 0.7962 (m-10) REVERT: A 896 ASP cc_start: 0.8716 (p0) cc_final: 0.8274 (t0) REVERT: A 906 MET cc_start: 0.7348 (ttt) cc_final: 0.7112 (ttt) REVERT: A 1033 LEU cc_start: 0.9112 (tt) cc_final: 0.8777 (mp) REVERT: A 1172 PHE cc_start: 0.7911 (m-80) cc_final: 0.7676 (m-80) REVERT: B 668 LYS cc_start: 0.8795 (tptp) cc_final: 0.8314 (mmmt) REVERT: B 868 ASP cc_start: 0.8235 (m-30) cc_final: 0.7987 (p0) REVERT: B 942 ASN cc_start: 0.8550 (m-40) cc_final: 0.8082 (t0) REVERT: B 1090 GLU cc_start: 0.9207 (tp30) cc_final: 0.8866 (tp30) REVERT: B 1094 LEU cc_start: 0.9425 (mt) cc_final: 0.9209 (tp) REVERT: C 452 MET cc_start: 0.2635 (mtp) cc_final: 0.2249 (mtp) REVERT: C 563 MET cc_start: 0.1769 (tpt) cc_final: 0.0960 (tpt) REVERT: C 661 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7946 (m) REVERT: C 794 TYR cc_start: 0.7857 (t80) cc_final: 0.7629 (t80) REVERT: C 807 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7687 (pttm) REVERT: C 815 GLN cc_start: 0.8654 (mt0) cc_final: 0.8189 (tm-30) REVERT: C 831 ILE cc_start: 0.9061 (mm) cc_final: 0.8853 (mm) REVERT: C 833 GLN cc_start: 0.9097 (tt0) cc_final: 0.8691 (tp40) REVERT: C 843 ASP cc_start: 0.8091 (t70) cc_final: 0.7865 (t70) REVERT: C 913 MET cc_start: 0.8034 (tpt) cc_final: 0.7592 (ppp) REVERT: C 1069 ARG cc_start: 0.8848 (tpt-90) cc_final: 0.8225 (ptm160) REVERT: C 1105 GLU cc_start: 0.7942 (tp30) cc_final: 0.7680 (tp30) REVERT: C 1179 ARG cc_start: 0.6320 (mtt180) cc_final: 0.5938 (mtm-85) REVERT: C 1186 TYR cc_start: 0.6326 (m-80) cc_final: 0.5881 (m-10) outliers start: 7 outliers final: 1 residues processed: 466 average time/residue: 0.3737 time to fit residues: 280.6036 Evaluate side-chains 293 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 291 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 336 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 308 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN A1176 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 521 ASN ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 GLN C1104 ASN ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 27022 Z= 0.284 Angle : 0.973 14.336 36747 Z= 0.498 Chirality : 0.054 0.285 4131 Planarity : 0.006 0.111 4750 Dihedral : 7.809 54.990 3712 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.98 % Favored : 86.70 % Rotamer: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3392 helix: -0.74 (0.18), residues: 693 sheet: -0.57 (0.21), residues: 604 loop : -2.72 (0.12), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 310 HIS 0.004 0.001 HIS B1122 PHE 0.040 0.002 PHE C 341 TYR 0.026 0.002 TYR B 648 ARG 0.007 0.001 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.5143 (mp) cc_final: 0.4899 (mp) REVERT: A 366 PHE cc_start: 0.5343 (m-10) cc_final: 0.5053 (m-10) REVERT: A 682 ILE cc_start: 0.7839 (pt) cc_final: 0.7521 (tp) REVERT: A 715 LEU cc_start: 0.8661 (tt) cc_final: 0.6785 (tt) REVERT: A 757 MET cc_start: 0.8621 (tpt) cc_final: 0.8177 (tpp) REVERT: A 895 PHE cc_start: 0.9073 (m-80) cc_final: 0.8649 (m-10) REVERT: A 939 MET cc_start: 0.7983 (mmm) cc_final: 0.7610 (mmm) REVERT: A 940 ASP cc_start: 0.6608 (m-30) cc_final: 0.6192 (m-30) REVERT: B 84 MET cc_start: 0.7405 (ttp) cc_final: 0.7200 (mtm) REVERT: B 265 LEU cc_start: 0.7012 (mt) cc_final: 0.6801 (mp) REVERT: B 351 TYR cc_start: 0.8496 (m-80) cc_final: 0.7773 (m-80) REVERT: B 868 ASP cc_start: 0.8422 (m-30) cc_final: 0.8187 (p0) REVERT: B 942 ASN cc_start: 0.8299 (m-40) cc_final: 0.8046 (t0) REVERT: B 1090 GLU cc_start: 0.9235 (tp30) cc_final: 0.8823 (tp30) REVERT: C 347 LEU cc_start: 0.9161 (mm) cc_final: 0.8884 (mt) REVERT: C 563 MET cc_start: 0.1557 (tpt) cc_final: 0.0902 (tpt) REVERT: C 815 GLN cc_start: 0.8746 (mt0) cc_final: 0.8296 (tm-30) REVERT: C 833 GLN cc_start: 0.8938 (tt0) cc_final: 0.8590 (tp40) REVERT: C 895 PHE cc_start: 0.8046 (m-80) cc_final: 0.7725 (m-80) REVERT: C 913 MET cc_start: 0.7833 (tpt) cc_final: 0.7563 (ptt) REVERT: C 1089 SER cc_start: 0.9265 (t) cc_final: 0.8853 (p) REVERT: C 1105 GLU cc_start: 0.8003 (tp30) cc_final: 0.7112 (tp30) REVERT: C 1186 TYR cc_start: 0.6606 (m-80) cc_final: 0.5936 (m-10) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.3440 time to fit residues: 245.9335 Evaluate side-chains 289 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 161 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 312 optimal weight: 20.0000 chunk 330 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 295 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 501 ASN A 516 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN C 501 ASN ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 ASN C1084 GLN C1104 ASN C1129 ASN ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 27022 Z= 0.306 Angle : 0.961 13.410 36747 Z= 0.490 Chirality : 0.054 0.258 4131 Planarity : 0.006 0.103 4750 Dihedral : 7.550 51.032 3712 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.07 % Favored : 86.67 % Rotamer: Outliers : 0.17 % Allowed : 2.36 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.13), residues: 3392 helix: -0.42 (0.19), residues: 684 sheet: -0.94 (0.21), residues: 631 loop : -2.62 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 310 HIS 0.005 0.001 HIS A 670 PHE 0.039 0.002 PHE A 895 TYR 0.044 0.002 TYR A 648 ARG 0.012 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 375 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 614 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8074 (mmm-85) REVERT: A 757 MET cc_start: 0.8714 (tpt) cc_final: 0.8196 (tpp) REVERT: A 820 LEU cc_start: 0.8357 (mt) cc_final: 0.8103 (tp) REVERT: A 939 MET cc_start: 0.8044 (mmm) cc_final: 0.7677 (mmm) REVERT: A 940 ASP cc_start: 0.6904 (m-30) cc_final: 0.6393 (m-30) REVERT: A 1172 PHE cc_start: 0.8106 (m-80) cc_final: 0.7795 (m-80) REVERT: B 696 MET cc_start: 0.7847 (mmm) cc_final: 0.7496 (mmm) REVERT: B 711 VAL cc_start: 0.7199 (t) cc_final: 0.6605 (t) REVERT: B 717 LEU cc_start: 0.6116 (tp) cc_final: 0.5905 (tp) REVERT: B 824 TYR cc_start: 0.8391 (m-80) cc_final: 0.8181 (m-80) REVERT: B 868 ASP cc_start: 0.8429 (m-30) cc_final: 0.8150 (p0) REVERT: B 942 ASN cc_start: 0.8474 (m-40) cc_final: 0.8254 (t0) REVERT: B 1090 GLU cc_start: 0.9187 (tp30) cc_final: 0.8908 (tp30) REVERT: C 501 ASN cc_start: 0.5700 (OUTLIER) cc_final: 0.4123 (t0) REVERT: C 563 MET cc_start: 0.1706 (tpt) cc_final: 0.1056 (tpt) REVERT: C 807 LYS cc_start: 0.8312 (tmtt) cc_final: 0.7511 (pttm) REVERT: C 815 GLN cc_start: 0.8811 (mt0) cc_final: 0.8299 (tm-30) REVERT: C 831 ILE cc_start: 0.9050 (mm) cc_final: 0.8766 (mm) REVERT: C 833 GLN cc_start: 0.8866 (tt0) cc_final: 0.8651 (tp40) REVERT: C 842 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8700 (tm-30) REVERT: C 913 MET cc_start: 0.7864 (tpt) cc_final: 0.7606 (ptt) REVERT: C 1179 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6426 (mtm-85) REVERT: C 1186 TYR cc_start: 0.6690 (m-10) cc_final: 0.6314 (m-10) outliers start: 5 outliers final: 0 residues processed: 380 average time/residue: 0.3488 time to fit residues: 215.5997 Evaluate side-chains 270 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 50.0000 chunk 187 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 282 optimal weight: 0.8980 chunk 228 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 168 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN A1146 HIS B 91 HIS B 501 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 HIS ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 436 ASN C 501 ASN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 27022 Z= 0.370 Angle : 0.995 13.714 36747 Z= 0.509 Chirality : 0.055 0.324 4131 Planarity : 0.006 0.105 4750 Dihedral : 7.618 48.063 3712 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.72 % Favored : 85.93 % Rotamer: Outliers : 0.07 % Allowed : 2.30 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.13), residues: 3392 helix: -0.65 (0.18), residues: 697 sheet: -1.00 (0.21), residues: 611 loop : -2.65 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 310 HIS 0.006 0.001 HIS A 670 PHE 0.072 0.003 PHE A 764 TYR 0.059 0.003 TYR B 648 ARG 0.012 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 341 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 691 ARG cc_start: 0.6774 (tpp80) cc_final: 0.6494 (tpp80) REVERT: A 757 MET cc_start: 0.8583 (tpt) cc_final: 0.8044 (tpp) REVERT: A 939 MET cc_start: 0.8071 (mmm) cc_final: 0.7792 (mmm) REVERT: A 940 ASP cc_start: 0.7458 (m-30) cc_final: 0.6744 (m-30) REVERT: A 1172 PHE cc_start: 0.8116 (m-80) cc_final: 0.7903 (m-80) REVERT: B 696 MET cc_start: 0.7982 (mmm) cc_final: 0.7636 (mmm) REVERT: B 824 TYR cc_start: 0.8424 (m-80) cc_final: 0.7956 (m-80) REVERT: B 868 ASP cc_start: 0.8745 (m-30) cc_final: 0.8278 (p0) REVERT: C 501 ASN cc_start: 0.5844 (OUTLIER) cc_final: 0.3811 (t0) REVERT: C 563 MET cc_start: 0.0401 (tpt) cc_final: -0.0062 (tpt) REVERT: C 778 PHE cc_start: 0.8828 (m-10) cc_final: 0.8551 (m-80) REVERT: C 815 GLN cc_start: 0.8854 (mt0) cc_final: 0.8332 (tm-30) REVERT: C 831 ILE cc_start: 0.9069 (mm) cc_final: 0.8742 (mm) REVERT: C 842 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 939 MET cc_start: 0.8228 (mtt) cc_final: 0.7983 (mtp) REVERT: C 1008 MET cc_start: 0.9006 (tmm) cc_final: 0.8680 (tmm) REVERT: C 1186 TYR cc_start: 0.6593 (m-10) cc_final: 0.6340 (m-10) outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.3617 time to fit residues: 203.4845 Evaluate side-chains 243 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 81 optimal weight: 0.0870 chunk 330 optimal weight: 0.7980 chunk 274 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27022 Z= 0.241 Angle : 0.914 12.584 36747 Z= 0.463 Chirality : 0.052 0.292 4131 Planarity : 0.006 0.104 4750 Dihedral : 7.158 42.221 3712 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.80 % Favored : 86.96 % Rotamer: Outliers : 0.07 % Allowed : 1.40 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 3392 helix: -0.36 (0.19), residues: 690 sheet: -0.93 (0.22), residues: 605 loop : -2.55 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 310 HIS 0.004 0.001 HIS A1122 PHE 0.056 0.002 PHE A 764 TYR 0.052 0.002 TYR C 648 ARG 0.012 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 361 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 261 GLN cc_start: 0.5605 (mp10) cc_final: 0.5044 (mp10) REVERT: A 691 ARG cc_start: 0.6542 (tpp80) cc_final: 0.6304 (tpp80) REVERT: A 757 MET cc_start: 0.8572 (tpt) cc_final: 0.8092 (tpp) REVERT: A 842 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 940 ASP cc_start: 0.7136 (m-30) cc_final: 0.6725 (m-30) REVERT: A 1090 GLU cc_start: 0.9377 (mp0) cc_final: 0.9154 (mp0) REVERT: A 1172 PHE cc_start: 0.8007 (m-80) cc_final: 0.7723 (m-80) REVERT: B 616 VAL cc_start: 0.8106 (m) cc_final: 0.7846 (p) REVERT: B 696 MET cc_start: 0.7916 (mmm) cc_final: 0.7529 (mmm) REVERT: B 824 TYR cc_start: 0.8338 (m-80) cc_final: 0.7707 (m-80) REVERT: B 831 ILE cc_start: 0.9524 (mm) cc_final: 0.9302 (mm) REVERT: B 868 ASP cc_start: 0.8567 (m-30) cc_final: 0.8073 (p0) REVERT: B 1067 ILE cc_start: 0.9000 (mt) cc_final: 0.8657 (tp) REVERT: C 71 TYR cc_start: 0.7282 (t80) cc_final: 0.7066 (t80) REVERT: C 501 ASN cc_start: 0.5743 (OUTLIER) cc_final: 0.3736 (t0) REVERT: C 563 MET cc_start: 0.0650 (tpt) cc_final: 0.0086 (tpt) REVERT: C 778 PHE cc_start: 0.8887 (m-10) cc_final: 0.8550 (m-80) REVERT: C 786 PHE cc_start: 0.8564 (m-80) cc_final: 0.8212 (m-80) REVERT: C 815 GLN cc_start: 0.8818 (mt0) cc_final: 0.8307 (tm-30) REVERT: C 820 LEU cc_start: 0.8742 (mt) cc_final: 0.8536 (mt) REVERT: C 831 ILE cc_start: 0.9002 (mm) cc_final: 0.8709 (mm) REVERT: C 842 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8750 (tm-30) REVERT: C 1008 MET cc_start: 0.9031 (tmm) cc_final: 0.8785 (tmm) REVERT: C 1186 TYR cc_start: 0.6513 (m-10) cc_final: 0.6073 (m-10) outliers start: 2 outliers final: 0 residues processed: 363 average time/residue: 0.3475 time to fit residues: 204.9641 Evaluate side-chains 265 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 188 optimal weight: 7.9990 chunk 241 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 278 optimal weight: 50.0000 chunk 184 optimal weight: 0.9990 chunk 329 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN B 486 HIS B 501 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27022 Z= 0.251 Angle : 0.909 14.198 36747 Z= 0.460 Chirality : 0.052 0.305 4131 Planarity : 0.006 0.111 4750 Dihedral : 7.022 39.553 3712 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.24 % Favored : 86.52 % Rotamer: Outliers : 0.10 % Allowed : 1.10 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3392 helix: -0.28 (0.19), residues: 696 sheet: -0.94 (0.21), residues: 650 loop : -2.59 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 310 HIS 0.012 0.001 HIS B 486 PHE 0.031 0.002 PHE A 764 TYR 0.041 0.002 TYR C 648 ARG 0.012 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 338 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 261 GLN cc_start: 0.5602 (mp10) cc_final: 0.5083 (mp10) REVERT: A 367 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 648 TYR cc_start: 0.7754 (t80) cc_final: 0.7509 (t80) REVERT: A 691 ARG cc_start: 0.6541 (tpp80) cc_final: 0.6186 (tpp80) REVERT: A 757 MET cc_start: 0.8532 (tpt) cc_final: 0.8073 (tpp) REVERT: A 817 CYS cc_start: 0.5028 (m) cc_final: 0.4773 (m) REVERT: A 820 LEU cc_start: 0.8691 (mt) cc_final: 0.8342 (tp) REVERT: A 842 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 940 ASP cc_start: 0.7181 (m-30) cc_final: 0.6417 (m-30) REVERT: B 616 VAL cc_start: 0.8038 (m) cc_final: 0.7768 (p) REVERT: B 696 MET cc_start: 0.7923 (mmm) cc_final: 0.7546 (mmm) REVERT: B 777 TYR cc_start: 0.8180 (m-80) cc_final: 0.7861 (m-80) REVERT: B 831 ILE cc_start: 0.9540 (mm) cc_final: 0.9312 (mm) REVERT: B 868 ASP cc_start: 0.8596 (m-30) cc_final: 0.8099 (p0) REVERT: B 938 LEU cc_start: 0.8970 (tt) cc_final: 0.8433 (tt) REVERT: B 1067 ILE cc_start: 0.8995 (mt) cc_final: 0.8719 (tp) REVERT: B 1105 GLU cc_start: 0.8654 (tp30) cc_final: 0.8331 (tp30) REVERT: C 361 TYR cc_start: 0.8511 (m-10) cc_final: 0.8302 (m-10) REVERT: C 738 LEU cc_start: 0.7919 (mt) cc_final: 0.7676 (mt) REVERT: C 778 PHE cc_start: 0.8847 (m-10) cc_final: 0.8535 (m-80) REVERT: C 786 PHE cc_start: 0.8529 (m-80) cc_final: 0.8213 (m-80) REVERT: C 815 GLN cc_start: 0.8783 (mt0) cc_final: 0.8311 (tm-30) REVERT: C 831 ILE cc_start: 0.9018 (mm) cc_final: 0.8704 (mm) REVERT: C 833 GLN cc_start: 0.8584 (tp40) cc_final: 0.8229 (tp-100) REVERT: C 1008 MET cc_start: 0.8986 (tmm) cc_final: 0.8756 (tmm) REVERT: C 1058 LEU cc_start: 0.7151 (pp) cc_final: 0.6837 (tp) REVERT: C 1179 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6690 (mtm-85) REVERT: C 1186 TYR cc_start: 0.6264 (m-10) cc_final: 0.6055 (m-10) outliers start: 3 outliers final: 2 residues processed: 341 average time/residue: 0.3618 time to fit residues: 200.6865 Evaluate side-chains 248 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 162 optimal weight: 50.0000 chunk 30 optimal weight: 0.9980 chunk 259 optimal weight: 0.8980 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27022 Z= 0.247 Angle : 0.904 16.334 36747 Z= 0.458 Chirality : 0.052 0.301 4131 Planarity : 0.006 0.109 4750 Dihedral : 6.901 36.718 3712 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.24 % Favored : 86.55 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.14), residues: 3392 helix: -0.25 (0.19), residues: 701 sheet: -0.95 (0.21), residues: 647 loop : -2.54 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 310 HIS 0.011 0.001 HIS C 486 PHE 0.046 0.002 PHE A 764 TYR 0.031 0.002 TYR B1171 ARG 0.015 0.001 ARG C 887 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 261 GLN cc_start: 0.5671 (mp10) cc_final: 0.5146 (mp10) REVERT: A 691 ARG cc_start: 0.6846 (tpp80) cc_final: 0.6336 (tpp80) REVERT: A 757 MET cc_start: 0.8626 (tpt) cc_final: 0.8241 (tpp) REVERT: A 906 MET cc_start: 0.7216 (mtp) cc_final: 0.6557 (mmm) REVERT: A 940 ASP cc_start: 0.7608 (m-30) cc_final: 0.7378 (t0) REVERT: B 616 VAL cc_start: 0.8068 (m) cc_final: 0.7813 (p) REVERT: B 696 MET cc_start: 0.7912 (mmm) cc_final: 0.7637 (mmm) REVERT: B 777 TYR cc_start: 0.8175 (m-80) cc_final: 0.7866 (m-80) REVERT: B 831 ILE cc_start: 0.9500 (mm) cc_final: 0.9260 (mm) REVERT: B 913 MET cc_start: 0.7760 (tpt) cc_final: 0.7425 (ttt) REVERT: B 939 MET cc_start: 0.8692 (mmm) cc_final: 0.8488 (mmm) REVERT: B 1067 ILE cc_start: 0.9003 (mt) cc_final: 0.8725 (tp) REVERT: C 361 TYR cc_start: 0.8544 (m-10) cc_final: 0.8270 (m-10) REVERT: C 563 MET cc_start: 0.0912 (tpt) cc_final: 0.0136 (tpt) REVERT: C 696 MET cc_start: 0.7595 (mtp) cc_final: 0.7125 (tpp) REVERT: C 778 PHE cc_start: 0.8791 (m-10) cc_final: 0.8500 (m-80) REVERT: C 786 PHE cc_start: 0.8529 (m-80) cc_final: 0.8224 (m-80) REVERT: C 815 GLN cc_start: 0.8821 (mt0) cc_final: 0.8343 (tm-30) REVERT: C 831 ILE cc_start: 0.9000 (mm) cc_final: 0.8701 (mm) REVERT: C 1008 MET cc_start: 0.9002 (tmm) cc_final: 0.8788 (tmm) REVERT: C 1105 GLU cc_start: 0.8078 (tp30) cc_final: 0.7777 (tp30) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.3736 time to fit residues: 203.8134 Evaluate side-chains 250 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 9.9990 chunk 315 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 277 optimal weight: 50.0000 chunk 290 optimal weight: 30.0000 chunk 306 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27022 Z= 0.298 Angle : 0.936 15.813 36747 Z= 0.475 Chirality : 0.053 0.332 4131 Planarity : 0.006 0.107 4750 Dihedral : 7.017 35.896 3712 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.72 % Favored : 86.08 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.14), residues: 3392 helix: -0.32 (0.19), residues: 702 sheet: -1.08 (0.22), residues: 590 loop : -2.55 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 310 HIS 0.006 0.001 HIS A 81 PHE 0.032 0.002 PHE A 323 TYR 0.045 0.002 TYR C 648 ARG 0.014 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 261 GLN cc_start: 0.5954 (mp10) cc_final: 0.5336 (mp10) REVERT: A 627 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8016 (tp40) REVERT: A 691 ARG cc_start: 0.6795 (tpp80) cc_final: 0.6276 (tpp80) REVERT: A 738 LEU cc_start: 0.7656 (mt) cc_final: 0.7398 (mt) REVERT: A 757 MET cc_start: 0.8627 (tpt) cc_final: 0.8299 (tpp) REVERT: A 817 CYS cc_start: 0.4982 (m) cc_final: 0.4773 (m) REVERT: A 842 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 844 ASP cc_start: 0.9008 (m-30) cc_final: 0.8779 (m-30) REVERT: A 906 MET cc_start: 0.7343 (mtp) cc_final: 0.6632 (mmm) REVERT: B 616 VAL cc_start: 0.8191 (m) cc_final: 0.7982 (p) REVERT: B 696 MET cc_start: 0.8020 (mmm) cc_final: 0.7730 (mmm) REVERT: B 778 PHE cc_start: 0.7216 (m-80) cc_final: 0.6904 (m-80) REVERT: B 831 ILE cc_start: 0.9482 (mm) cc_final: 0.9224 (mm) REVERT: B 913 MET cc_start: 0.7493 (tpt) cc_final: 0.7124 (ttt) REVERT: B 1067 ILE cc_start: 0.9028 (mt) cc_final: 0.8716 (tp) REVERT: B 1105 GLU cc_start: 0.8448 (tp30) cc_final: 0.8091 (tp30) REVERT: B 1184 TRP cc_start: 0.7111 (p-90) cc_final: 0.6826 (p-90) REVERT: C 361 TYR cc_start: 0.8612 (m-10) cc_final: 0.8331 (m-10) REVERT: C 563 MET cc_start: 0.0925 (tpt) cc_final: 0.0076 (tpt) REVERT: C 696 MET cc_start: 0.7615 (mtp) cc_final: 0.7167 (tpp) REVERT: C 778 PHE cc_start: 0.8711 (m-10) cc_final: 0.8373 (m-10) REVERT: C 786 PHE cc_start: 0.8594 (m-80) cc_final: 0.8373 (m-80) REVERT: C 807 LYS cc_start: 0.8387 (tmtt) cc_final: 0.7583 (pttm) REVERT: C 815 GLN cc_start: 0.8865 (mt0) cc_final: 0.8366 (tm-30) REVERT: C 831 ILE cc_start: 0.9051 (mm) cc_final: 0.8736 (mm) REVERT: C 842 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8851 (tm-30) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.3632 time to fit residues: 189.3164 Evaluate side-chains 247 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 225 optimal weight: 0.0030 chunk 340 optimal weight: 7.9990 chunk 313 optimal weight: 20.0000 chunk 271 optimal weight: 40.0000 chunk 28 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 GLN ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27022 Z= 0.216 Angle : 0.886 14.767 36747 Z= 0.447 Chirality : 0.051 0.286 4131 Planarity : 0.006 0.112 4750 Dihedral : 6.695 34.607 3712 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.92 % Favored : 86.91 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 3392 helix: -0.21 (0.19), residues: 705 sheet: -1.21 (0.20), residues: 687 loop : -2.53 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 253 HIS 0.005 0.001 HIS A1122 PHE 0.031 0.002 PHE A 323 TYR 0.036 0.002 TYR B1171 ARG 0.014 0.001 ARG B 841 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 GLN cc_start: 0.5609 (mp10) cc_final: 0.5100 (mp10) REVERT: A 691 ARG cc_start: 0.7108 (tpp80) cc_final: 0.6687 (tpp80) REVERT: A 738 LEU cc_start: 0.7631 (mt) cc_final: 0.7428 (mt) REVERT: A 757 MET cc_start: 0.8482 (tpt) cc_final: 0.8266 (tpp) REVERT: A 817 CYS cc_start: 0.4958 (m) cc_final: 0.4716 (m) REVERT: A 906 MET cc_start: 0.7421 (mtp) cc_final: 0.6823 (mmm) REVERT: A 943 MET cc_start: 0.7799 (ttm) cc_final: 0.6982 (tpp) REVERT: B 696 MET cc_start: 0.7749 (mmm) cc_final: 0.7512 (mmm) REVERT: B 777 TYR cc_start: 0.8203 (m-80) cc_final: 0.7860 (m-80) REVERT: B 778 PHE cc_start: 0.7035 (m-80) cc_final: 0.6800 (m-80) REVERT: B 831 ILE cc_start: 0.9474 (mm) cc_final: 0.9233 (mm) REVERT: B 854 LYS cc_start: 0.7859 (pptt) cc_final: 0.7315 (pptt) REVERT: B 913 MET cc_start: 0.7383 (tpt) cc_final: 0.6973 (ttt) REVERT: B 1067 ILE cc_start: 0.8961 (mt) cc_final: 0.8700 (tp) REVERT: B 1090 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8846 (tp30) REVERT: B 1105 GLU cc_start: 0.8347 (tp30) cc_final: 0.7977 (tp30) REVERT: C 278 MET cc_start: 0.6900 (ttm) cc_final: 0.6403 (ttp) REVERT: C 361 TYR cc_start: 0.8532 (m-10) cc_final: 0.8310 (m-10) REVERT: C 563 MET cc_start: 0.1759 (tpt) cc_final: 0.0811 (tpt) REVERT: C 696 MET cc_start: 0.7509 (mtp) cc_final: 0.7203 (tpp) REVERT: C 722 LEU cc_start: 0.8334 (pp) cc_final: 0.8006 (tp) REVERT: C 778 PHE cc_start: 0.8636 (m-10) cc_final: 0.8380 (m-10) REVERT: C 815 GLN cc_start: 0.8775 (mt0) cc_final: 0.8313 (tm-30) REVERT: C 831 ILE cc_start: 0.9015 (mm) cc_final: 0.8756 (mm) REVERT: C 833 GLN cc_start: 0.9212 (mt0) cc_final: 0.8987 (mt0) REVERT: C 1105 GLU cc_start: 0.7903 (tp30) cc_final: 0.7635 (tp30) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3623 time to fit residues: 198.9373 Evaluate side-chains 251 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 75 optimal weight: 4.9990 chunk 271 optimal weight: 0.0470 chunk 113 optimal weight: 0.0040 chunk 279 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 overall best weight: 2.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.127427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.108323 restraints weight = 203123.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.107156 restraints weight = 192053.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.108797 restraints weight = 154338.132| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.7820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27022 Z= 0.225 Angle : 0.880 14.790 36747 Z= 0.443 Chirality : 0.051 0.289 4131 Planarity : 0.006 0.109 4750 Dihedral : 6.587 33.816 3712 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.04 % Favored : 86.82 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.14), residues: 3392 helix: -0.08 (0.19), residues: 698 sheet: -1.13 (0.21), residues: 677 loop : -2.53 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 310 HIS 0.005 0.001 HIS A1122 PHE 0.025 0.002 PHE A 323 TYR 0.034 0.002 TYR B1171 ARG 0.014 0.001 ARG B 841 =============================================================================== Job complete usr+sys time: 5532.47 seconds wall clock time: 101 minutes 30.08 seconds (6090.08 seconds total)