Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 10:57:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/04_2023/7l2j_23130_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11360 2.51 5 N 2780 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 280": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 651": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "B" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "C" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "D" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLU A 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 648 " occ=0.50 residue: pdb=" N AGLU B 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 648 " occ=0.50 residue: pdb=" N AGLU C 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU C 648 " occ=0.50 residue: pdb=" N AGLU D 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 648 " occ=0.50 Time building chain proxies: 17.92, per 1000 atoms: 1.03 Number of scatterers: 17336 At special positions: 0 Unit cell: (125.35, 125.35, 112.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3092 8.00 N 2780 7.00 C 11360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.39 Conformation dependent library (CDL) restraints added in 4.9 seconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 4 sheets defined 57.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.014A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.747A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 470 through 497 Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 537 through 556 removed outlier: 4.468A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.924A pdb=" N ASP A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.130A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 711 removed outlier: 3.783A pdb=" N ALA A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.597A pdb=" N LEU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.985A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 470 through 497 Processing helix chain 'B' and resid 503 through 506 No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.709A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 4.086A pdb=" N ASP B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.057A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 711 removed outlier: 3.756A pdb=" N ALA B 690 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 223 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.506A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 3.788A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 470 through 497 Processing helix chain 'C' and resid 503 through 506 No H-bonds generated for 'chain 'C' and resid 503 through 506' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 537 through 556 removed outlier: 3.587A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 4.207A pdb=" N ASP C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.215A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 711 removed outlier: 3.731A pdb=" N ALA C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.984A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.798A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 470 through 497 Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 537 through 556 removed outlier: 4.474A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.056A pdb=" N ASP D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.104A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 removed outlier: 3.519A pdb=" N ILE D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 711 removed outlier: 3.626A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 4.216A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 742 through 747 removed outlier: 4.041A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 742 through 747 removed outlier: 4.337A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 742 through 747 removed outlier: 4.258A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2490 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: 4.94 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2680 1.31 - 1.43: 5009 1.43 - 1.56: 9885 1.56 - 1.69: 10 1.69 - 1.81: 164 Bond restraints: 17748 Sorted by residual: bond pdb=" C ASP C 654 " pdb=" N PHE C 655 " ideal model delta sigma weight residual 1.333 1.234 0.099 1.29e-02 6.01e+03 5.87e+01 bond pdb=" C ASP D 654 " pdb=" N PHE D 655 " ideal model delta sigma weight residual 1.333 1.433 -0.100 1.42e-02 4.96e+03 4.99e+01 bond pdb=" C ASP B 654 " pdb=" N PHE B 655 " ideal model delta sigma weight residual 1.333 1.259 0.073 1.29e-02 6.01e+03 3.23e+01 bond pdb=" C TYR B 511 " pdb=" N SER B 512 " ideal model delta sigma weight residual 1.335 1.269 0.066 1.31e-02 5.83e+03 2.57e+01 bond pdb=" CA THR D 650 " pdb=" C THR D 650 " ideal model delta sigma weight residual 1.521 1.570 -0.049 1.24e-02 6.50e+03 1.56e+01 ... (remaining 17743 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.93: 263 105.93 - 112.96: 9408 112.96 - 119.99: 6745 119.99 - 127.02: 7451 127.02 - 134.05: 153 Bond angle restraints: 24020 Sorted by residual: angle pdb=" N ILE D 573 " pdb=" CA ILE D 573 " pdb=" C ILE D 573 " ideal model delta sigma weight residual 110.82 106.53 4.29 9.70e-01 1.06e+00 1.96e+01 angle pdb=" N GLU D 651 " pdb=" CA GLU D 651 " pdb=" C GLU D 651 " ideal model delta sigma weight residual 109.06 116.34 -7.28 1.70e+00 3.46e-01 1.84e+01 angle pdb=" C TYR C 511 " pdb=" N SER C 512 " pdb=" CA SER C 512 " ideal model delta sigma weight residual 120.82 127.01 -6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" N GLU B 651 " pdb=" CA GLU B 651 " pdb=" C GLU B 651 " ideal model delta sigma weight residual 109.23 114.83 -5.60 1.55e+00 4.16e-01 1.30e+01 angle pdb=" N GLU C 651 " pdb=" CA GLU C 651 " pdb=" C GLU C 651 " ideal model delta sigma weight residual 109.23 114.68 -5.45 1.55e+00 4.16e-01 1.24e+01 ... (remaining 24015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.49: 10010 19.49 - 38.97: 323 38.97 - 58.46: 68 58.46 - 77.94: 16 77.94 - 97.43: 11 Dihedral angle restraints: 10428 sinusoidal: 4184 harmonic: 6244 Sorted by residual: dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual 93.00 59.93 33.07 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CB CYS B 386 " pdb=" SG CYS B 386 " pdb=" SG CYS B 390 " pdb=" CB CYS B 390 " ideal model delta sinusoidal sigma weight residual 93.00 59.94 33.06 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 60.29 32.71 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 10425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 2700 1.008 - 2.015: 0 2.015 - 3.023: 0 3.023 - 4.031: 0 4.031 - 5.038: 8 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C3 XJ7 D 901 " pdb=" C2 XJ7 D 901 " pdb=" C24 XJ7 D 901 " pdb=" O3 XJ7 D 901 " both_signs ideal model delta sigma weight residual False -2.50 2.54 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C3 XJ7 A 901 " pdb=" C2 XJ7 A 901 " pdb=" C24 XJ7 A 901 " pdb=" O3 XJ7 A 901 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.04 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" C3 XJ7 C 901 " pdb=" C2 XJ7 C 901 " pdb=" C24 XJ7 C 901 " pdb=" O3 XJ7 C 901 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.04 2.00e-01 2.50e+01 6.34e+02 ... (remaining 2705 not shown) Planarity restraints: 2964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 649 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C PHE D 649 " 0.054 2.00e-02 2.50e+03 pdb=" O PHE D 649 " -0.020 2.00e-02 2.50e+03 pdb=" N THR D 650 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 649 " -0.012 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PHE B 649 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE B 649 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 650 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C GLY B 548 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY B 548 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP B 549 " -0.013 2.00e-02 2.50e+03 ... (remaining 2961 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 184 2.64 - 3.20: 16845 3.20 - 3.77: 26004 3.77 - 4.33: 35647 4.33 - 4.90: 58920 Nonbonded interactions: 137600 Sorted by model distance: nonbonded pdb=" OG SER B 722 " pdb=" O CYS B 741 " model vdw 2.074 2.440 nonbonded pdb=" O ILE A 672 " pdb=" ND2 ASN A 676 " model vdw 2.173 2.520 nonbonded pdb=" O ILE C 672 " pdb=" ND2 ASN C 676 " model vdw 2.174 2.520 nonbonded pdb=" O ILE B 672 " pdb=" ND2 ASN B 676 " model vdw 2.205 2.520 nonbonded pdb=" NZ LYS B 425 " pdb=" OE1 GLU B 709 " model vdw 2.216 2.520 ... (remaining 137595 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 198 through 647 or resid 649 through 749 or resid 901)) selection = (chain 'B' and (resid 198 through 647 or resid 649 through 749 or resid 901)) selection = (chain 'C' and (resid 198 through 647 or resid 649 through 749 or resid 901)) selection = (chain 'D' and (resid 198 through 647 or resid 649 through 749 or resid 901)) } 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=0.50 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.110 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 57.140 Find NCS groups from input model: 1.240 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: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.100 17748 Z= 0.438 Angle : 0.705 7.283 24020 Z= 0.399 Chirality : 0.276 5.038 2708 Planarity : 0.004 0.031 2964 Dihedral : 11.484 97.428 6408 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2112 helix: 1.72 (0.14), residues: 1224 sheet: -0.22 (0.54), residues: 56 loop : -1.51 (0.22), residues: 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 724 time to evaluate : 2.088 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 outliers start: 3 outliers final: 0 residues processed: 725 average time/residue: 0.3434 time to fit residues: 354.6628 Evaluate side-chains 440 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 188 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN B 202 GLN B 270 ASN B 364 HIS ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 270 ASN C 408 ASN C 494 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 494 GLN D 533 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17748 Z= 0.188 Angle : 0.626 8.601 24020 Z= 0.324 Chirality : 0.042 0.276 2708 Planarity : 0.004 0.055 2964 Dihedral : 7.059 67.644 2396 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 2112 helix: 1.84 (0.15), residues: 1248 sheet: -0.17 (0.56), residues: 56 loop : -1.85 (0.21), residues: 808 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 476 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 26 residues processed: 504 average time/residue: 0.2854 time to fit residues: 219.4283 Evaluate side-chains 437 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 411 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1586 time to fit residues: 10.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 chunk 189 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 289 HIS ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 206 HIS C 289 HIS C 423 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 17748 Z= 0.241 Angle : 0.646 18.850 24020 Z= 0.324 Chirality : 0.040 0.182 2708 Planarity : 0.004 0.056 2964 Dihedral : 6.772 54.984 2396 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2112 helix: 1.59 (0.15), residues: 1260 sheet: 0.08 (0.56), residues: 56 loop : -1.94 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 429 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 27 residues processed: 443 average time/residue: 0.2965 time to fit residues: 197.4393 Evaluate side-chains 419 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 392 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2065 time to fit residues: 12.3214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.0670 chunk 142 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS A 494 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 17748 Z= 0.163 Angle : 0.604 15.349 24020 Z= 0.305 Chirality : 0.038 0.157 2708 Planarity : 0.003 0.038 2964 Dihedral : 6.556 54.641 2396 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2112 helix: 1.58 (0.15), residues: 1260 sheet: 0.08 (0.58), residues: 56 loop : -1.97 (0.20), residues: 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 425 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 442 average time/residue: 0.2914 time to fit residues: 196.0889 Evaluate side-chains 413 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 397 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1630 time to fit residues: 7.8619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 494 GLN A 560 GLN B 206 HIS B 232 ASN C 232 ASN C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS D 228 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 17748 Z= 0.415 Angle : 0.735 15.947 24020 Z= 0.371 Chirality : 0.044 0.174 2708 Planarity : 0.004 0.042 2964 Dihedral : 6.935 54.063 2396 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2112 helix: 1.10 (0.14), residues: 1264 sheet: 0.49 (0.62), residues: 56 loop : -2.07 (0.21), residues: 792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 427 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 27 residues processed: 442 average time/residue: 0.3045 time to fit residues: 204.1107 Evaluate side-chains 420 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 393 time to evaluate : 2.150 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1689 time to fit residues: 11.2135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 17748 Z= 0.186 Angle : 0.647 16.329 24020 Z= 0.326 Chirality : 0.040 0.253 2708 Planarity : 0.004 0.055 2964 Dihedral : 6.730 55.684 2396 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2112 helix: 1.34 (0.14), residues: 1264 sheet: 0.49 (0.63), residues: 56 loop : -2.07 (0.21), residues: 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 408 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 419 average time/residue: 0.3039 time to fit residues: 192.6296 Evaluate side-chains 404 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 393 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1683 time to fit residues: 6.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17748 Z= 0.182 Angle : 0.631 15.394 24020 Z= 0.315 Chirality : 0.040 0.246 2708 Planarity : 0.004 0.054 2964 Dihedral : 6.474 52.151 2396 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.18 (0.18), residues: 2112 helix: 1.37 (0.15), residues: 1264 sheet: 0.61 (0.64), residues: 56 loop : -2.08 (0.21), residues: 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 411 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 416 average time/residue: 0.2873 time to fit residues: 181.6030 Evaluate side-chains 407 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 393 time to evaluate : 2.027 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1672 time to fit residues: 7.1481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17748 Z= 0.202 Angle : 0.641 15.973 24020 Z= 0.320 Chirality : 0.040 0.206 2708 Planarity : 0.003 0.054 2964 Dihedral : 6.350 49.992 2396 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.16 (0.18), residues: 2112 helix: 1.37 (0.15), residues: 1260 sheet: 0.60 (0.63), residues: 56 loop : -2.09 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 407 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 412 average time/residue: 0.2870 time to fit residues: 181.4094 Evaluate side-chains 403 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 393 time to evaluate : 2.078 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1671 time to fit residues: 6.1491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.0970 chunk 192 optimal weight: 1.9990 chunk 175 optimal weight: 0.0670 chunk 186 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17748 Z= 0.180 Angle : 0.643 15.510 24020 Z= 0.317 Chirality : 0.040 0.291 2708 Planarity : 0.003 0.067 2964 Dihedral : 6.194 48.219 2396 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.22 (0.19), residues: 2112 helix: 1.41 (0.15), residues: 1260 sheet: 0.69 (0.63), residues: 56 loop : -2.06 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 408 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 413 average time/residue: 0.2819 time to fit residues: 178.6123 Evaluate side-chains 391 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 385 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2132 time to fit residues: 4.8004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 0.0370 chunk 137 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 17748 Z= 0.209 Angle : 0.665 17.292 24020 Z= 0.326 Chirality : 0.041 0.322 2708 Planarity : 0.004 0.060 2964 Dihedral : 6.160 47.960 2396 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.23 (0.18), residues: 2112 helix: 1.45 (0.15), residues: 1240 sheet: 0.69 (0.62), residues: 56 loop : -2.02 (0.21), residues: 816 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 403 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 406 average time/residue: 0.2855 time to fit residues: 179.1397 Evaluate side-chains 394 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1609 time to fit residues: 3.1488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 24 optimal weight: 0.0670 chunk 45 optimal weight: 0.0050 chunk 165 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.197323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135820 restraints weight = 60560.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138703 restraints weight = 22426.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139666 restraints weight = 14212.312| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17748 Z= 0.173 Angle : 0.668 16.757 24020 Z= 0.328 Chirality : 0.041 0.326 2708 Planarity : 0.003 0.041 2964 Dihedral : 6.029 48.476 2396 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.32 (0.19), residues: 2112 helix: 1.52 (0.15), residues: 1240 sheet: 0.69 (0.63), residues: 56 loop : -2.00 (0.21), residues: 816 =============================================================================== Job complete usr+sys time: 4169.04 seconds wall clock time: 75 minutes 58.49 seconds (4558.49 seconds total)