Starting phenix.real_space_refine on Mon Dec 11 09:11:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_2023/7l2j_23130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_2023/7l2j_23130.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_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_23130/12_2023/7l2j_23130_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_2023/7l2j_23130_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_2023/7l2j_23130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_2023/7l2j_23130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_2023/7l2j_23130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/12_2023/7l2j_23130_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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-1.21rc1-5172/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: 16.96, per 1000 atoms: 0.98 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: 6.57 Conformation dependent library (CDL) restraints added in 5.9 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: 3.47 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: 5.04 Time building geometry restraints manager: 7.10 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 - 35.86: 10348 35.86 - 71.71: 100 71.71 - 107.57: 15 107.57 - 143.42: 0 143.42 - 179.28: 1 Dihedral angle restraints: 10464 sinusoidal: 4220 harmonic: 6244 Sorted by residual: dihedral pdb=" CB BGLU D 648 " pdb=" CG BGLU D 648 " pdb=" CD BGLU D 648 " pdb=" OE1BGLU D 648 " ideal model delta sinusoidal sigma weight residual 0.00 179.28 -179.28 1 3.00e+01 1.11e-03 2.13e+01 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 ... (remaining 10461 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: 0.820 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: 3.560 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 57.930 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.140 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.670 ------------------------------------------------------------------------------- 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 : 11.794 179.276 6444 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 % Allowed : 1.45 % Favored : 98.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 697 HIS 0.004 0.001 HIS B 364 PHE 0.016 0.002 PHE C 236 TYR 0.017 0.002 TYR C 565 ARG 0.004 0.001 ARG A 721 *********************** 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 : 1.793 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: 0.3292 time to fit residues: 340.3436 Evaluate side-chains 440 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9037 ------------------------------------------------------------------------------- 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 494 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 494 GLN ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17748 Z= 0.190 Angle : 0.632 8.673 24020 Z= 0.327 Chirality : 0.042 0.266 2708 Planarity : 0.004 0.058 2964 Dihedral : 8.335 69.039 2432 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.31 % Allowed : 13.95 % Favored : 83.74 % 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: 0.67 (0.19), residues: 2112 helix: 1.84 (0.15), residues: 1248 sheet: -0.13 (0.56), residues: 56 loop : -1.85 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 697 HIS 0.008 0.001 HIS A 364 PHE 0.053 0.002 PHE C 304 TYR 0.019 0.001 TYR C 351 ARG 0.010 0.001 ARG D 701 *********************** 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 517 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 474 time to evaluate : 1.783 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: 43 outliers final: 24 residues processed: 503 average time/residue: 0.2845 time to fit residues: 219.1715 Evaluate side-chains 435 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 411 time to evaluate : 1.974 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1649 time to fit residues: 10.1713 ------------------------------------------------------------------------------- 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: 6.9990 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 chunk 189 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 0.0970 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 408 ASN C 423 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17748 Z= 0.282 Angle : 0.657 17.351 24020 Z= 0.330 Chirality : 0.041 0.276 2708 Planarity : 0.004 0.056 2964 Dihedral : 7.617 55.068 2432 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.52 % Allowed : 16.68 % Favored : 80.79 % 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: 0.42 (0.18), residues: 2112 helix: 1.57 (0.15), residues: 1260 sheet: 0.15 (0.57), residues: 56 loop : -1.94 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 697 HIS 0.006 0.001 HIS C 289 PHE 0.033 0.002 PHE C 304 TYR 0.015 0.002 TYR C 495 ARG 0.006 0.001 ARG C 701 *********************** 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 475 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 428 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 31 residues processed: 445 average time/residue: 0.3134 time to fit residues: 209.9289 Evaluate side-chains 428 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 397 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1964 time to fit residues: 13.2583 ------------------------------------------------------------------------------- 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: 0.0010 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17748 Z= 0.174 Angle : 0.618 16.457 24020 Z= 0.311 Chirality : 0.039 0.287 2708 Planarity : 0.003 0.040 2964 Dihedral : 7.235 55.040 2432 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.66 % Allowed : 16.85 % Favored : 81.49 % 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: 0.38 (0.18), residues: 2112 helix: 1.55 (0.15), residues: 1260 sheet: 0.12 (0.57), residues: 56 loop : -1.96 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 697 HIS 0.005 0.001 HIS C 289 PHE 0.046 0.001 PHE B 304 TYR 0.018 0.001 TYR B 666 ARG 0.008 0.001 ARG D 701 *********************** 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 460 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 429 time to evaluate : 2.065 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: 31 outliers final: 15 residues processed: 443 average time/residue: 0.3035 time to fit residues: 205.1976 Evaluate side-chains 416 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 401 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1671 time to fit residues: 7.2912 ------------------------------------------------------------------------------- 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: 5.9990 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 206 HIS B 232 ASN B 560 GLN C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17748 Z= 0.287 Angle : 0.641 15.850 24020 Z= 0.326 Chirality : 0.041 0.246 2708 Planarity : 0.004 0.051 2964 Dihedral : 7.009 54.672 2432 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.04 % Allowed : 17.49 % Favored : 80.47 % 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: 0.21 (0.18), residues: 2112 helix: 1.36 (0.14), residues: 1264 sheet: 0.32 (0.60), residues: 56 loop : -1.98 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 697 HIS 0.003 0.001 HIS C 289 PHE 0.038 0.002 PHE B 304 TYR 0.027 0.002 TYR D 666 ARG 0.006 0.001 ARG D 701 *********************** 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 449 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 411 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 25 residues processed: 421 average time/residue: 0.2960 time to fit residues: 187.5238 Evaluate side-chains 413 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 388 time to evaluate : 1.976 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1854 time to fit residues: 11.8762 ------------------------------------------------------------------------------- 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: 0.0970 chunk 181 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 201 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 560 GLN C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17748 Z= 0.165 Angle : 0.616 15.838 24020 Z= 0.310 Chirality : 0.039 0.259 2708 Planarity : 0.003 0.040 2964 Dihedral : 6.728 57.095 2432 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.23 % Allowed : 18.19 % Favored : 80.58 % 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: 0.37 (0.18), residues: 2112 helix: 1.54 (0.15), residues: 1256 sheet: 0.40 (0.62), residues: 56 loop : -1.96 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 740 HIS 0.003 0.001 HIS C 289 PHE 0.038 0.001 PHE B 304 TYR 0.019 0.001 TYR D 666 ARG 0.009 0.001 ARG B 409 *********************** 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 435 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 412 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 417 average time/residue: 0.3028 time to fit residues: 189.1533 Evaluate side-chains 406 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 393 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2079 time to fit residues: 7.6746 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 146 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 200 optimal weight: 0.1980 chunk 125 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN D 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17748 Z= 0.194 Angle : 0.619 16.189 24020 Z= 0.311 Chirality : 0.039 0.315 2708 Planarity : 0.003 0.039 2964 Dihedral : 6.563 56.398 2432 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.50 % Allowed : 19.05 % Favored : 79.45 % 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: 0.31 (0.18), residues: 2112 helix: 1.49 (0.15), residues: 1260 sheet: 0.61 (0.64), residues: 56 loop : -2.03 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 697 HIS 0.003 0.001 HIS C 289 PHE 0.033 0.001 PHE B 304 TYR 0.015 0.001 TYR B 666 ARG 0.007 0.001 ARG B 739 *********************** 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 440 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 412 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 419 average time/residue: 0.2908 time to fit residues: 184.9417 Evaluate side-chains 412 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 401 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1638 time to fit residues: 6.1720 ------------------------------------------------------------------------------- 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: 0.0970 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 494 GLN D 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17748 Z= 0.188 Angle : 0.628 15.698 24020 Z= 0.317 Chirality : 0.040 0.353 2708 Planarity : 0.004 0.064 2964 Dihedral : 6.444 57.509 2432 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.91 % Allowed : 19.96 % Favored : 79.13 % 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: 0.26 (0.18), residues: 2112 helix: 1.43 (0.15), residues: 1260 sheet: 0.62 (0.64), residues: 56 loop : -2.02 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 697 HIS 0.002 0.001 HIS D 410 PHE 0.032 0.001 PHE B 304 TYR 0.050 0.001 TYR C 666 ARG 0.007 0.001 ARG D 499 *********************** 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 436 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 419 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 423 average time/residue: 0.3001 time to fit residues: 191.9931 Evaluate side-chains 417 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 408 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1778 time to fit residues: 5.6336 ------------------------------------------------------------------------------- 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: 0.7980 chunk 192 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 186 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 176 optimal weight: 0.1980 chunk 122 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** 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** D 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4267 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= 0.177 Angle : 0.649 16.437 24020 Z= 0.322 Chirality : 0.040 0.342 2708 Planarity : 0.003 0.059 2964 Dihedral : 6.340 58.644 2432 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.64 % Allowed : 20.87 % Favored : 78.49 % 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: 0.24 (0.18), residues: 2112 helix: 1.41 (0.15), residues: 1260 sheet: 0.65 (0.64), residues: 56 loop : -2.01 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 697 HIS 0.002 0.000 HIS D 364 PHE 0.032 0.001 PHE B 304 TYR 0.043 0.001 TYR C 666 ARG 0.012 0.001 ARG B 499 *********************** 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 424 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 412 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 416 average time/residue: 0.2842 time to fit residues: 181.1319 Evaluate side-chains 402 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 399 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2821 time to fit residues: 4.0723 ------------------------------------------------------------------------------- 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: 1.9990 chunk 120 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4373 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= 0.177 Angle : 0.646 16.056 24020 Z= 0.321 Chirality : 0.040 0.341 2708 Planarity : 0.003 0.037 2964 Dihedral : 6.244 59.936 2432 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.21 % Allowed : 22.05 % Favored : 77.74 % 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: 0.24 (0.18), residues: 2112 helix: 1.40 (0.15), residues: 1260 sheet: 0.67 (0.64), residues: 56 loop : -2.00 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 697 HIS 0.002 0.001 HIS D 364 PHE 0.030 0.001 PHE B 304 TYR 0.036 0.001 TYR C 666 ARG 0.025 0.001 ARG D 499 ********************** 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 409 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 405 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 406 average time/residue: 0.2875 time to fit residues: 179.2357 Evaluate side-chains 392 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1552 time to fit residues: 3.1592 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 145 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** 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** D 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.196739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135801 restraints weight = 60465.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137757 restraints weight = 23261.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138968 restraints weight = 14879.214| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 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 = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17748 Z= 0.177 Angle : 0.642 17.589 24020 Z= 0.318 Chirality : 0.040 0.321 2708 Planarity : 0.004 0.062 2964 Dihedral : 6.129 59.160 2432 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.11 % Allowed : 22.48 % Favored : 77.41 % 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: 0.26 (0.19), residues: 2112 helix: 1.41 (0.15), residues: 1260 sheet: 0.66 (0.65), residues: 56 loop : -1.98 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 697 HIS 0.002 0.001 HIS D 364 PHE 0.031 0.001 PHE B 304 TYR 0.031 0.001 TYR C 666 ARG 0.007 0.001 ARG B 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4266.32 seconds wall clock time: 77 minutes 49.86 seconds (4669.86 seconds total)