Starting phenix.real_space_refine on Thu Jun 12 00:58:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7t_28910/06_2025/8f7t_28910_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7t_28910/06_2025/8f7t_28910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7t_28910/06_2025/8f7t_28910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7t_28910/06_2025/8f7t_28910.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7t_28910/06_2025/8f7t_28910_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7t_28910/06_2025/8f7t_28910_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8376 2.51 5 N 2280 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13326 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3373 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 24, 'TRANS': 401} Chain breaks: 5 Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3373 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 24, 'TRANS': 401} Chain breaks: 5 Chain: "G" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3373 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 24, 'TRANS': 401} Chain breaks: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.86, per 1000 atoms: 0.66 Number of scatterers: 13326 At special positions: 0 Unit cell: (119.52, 127.82, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2562 8.00 N 2280 7.00 C 8376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=1.91 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.05 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 76 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 249 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 76 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 159 " distance=2.04 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 220 " - pdb=" SG CYS E 249 " distance=2.03 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 241 " distance=2.03 Simple disulfide: pdb=" SG CYS E 298 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 76 " distance=2.04 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 128 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 159 " distance=2.04 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 220 " - pdb=" SG CYS G 249 " distance=2.03 Simple disulfide: pdb=" SG CYS G 230 " - pdb=" SG CYS G 241 " distance=2.03 Simple disulfide: pdb=" SG CYS G 298 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-6 " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG C 601 " - " ASN C 291 " " NAG C 602 " - " ASN C 332 " " NAG C 603 " - " ASN C 132 " " NAG C 604 " - " ASN C 162 " " NAG E 601 " - " ASN E 291 " " NAG E 602 " - " ASN E 332 " " NAG E 603 " - " ASN E 132 " " NAG E 604 " - " ASN E 162 " " NAG G 601 " - " ASN G 291 " " NAG G 602 " - " ASN G 332 " " NAG G 603 " - " ASN G 132 " " NAG G 604 " - " ASN G 162 " " NAG I 1 " - " ASN C 448 " " NAG K 1 " - " ASN E 448 " " NAG L 1 " - " ASN G 448 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 25.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.145A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.503A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 595 removed outlier: 3.579A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.821A pdb=" N TRP A 614 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 4.263A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 658 Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.079A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 571 through 595 removed outlier: 3.521A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.645A pdb=" N TRP B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.288A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 100 through 118 removed outlier: 4.214A pdb=" N ASP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 352 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.989A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.347A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 486 " --> pdb=" O LEU C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 486' Processing helix chain 'D' and resid 524 through 528 removed outlier: 4.128A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.678A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 595 Processing helix chain 'D' and resid 611 through 615 removed outlier: 3.817A pdb=" N TRP D 614 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.853A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 636 Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 100 through 118 removed outlier: 4.214A pdb=" N ASP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 352 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.989A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 486 removed outlier: 4.347A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR E 486 " --> pdb=" O LEU E 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 482 through 486' Processing helix chain 'G' and resid 72 through 76 Processing helix chain 'G' and resid 100 through 118 removed outlier: 4.214A pdb=" N ASP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 352 Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.989A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 486 removed outlier: 4.347A pdb=" N LYS G 485 " --> pdb=" O GLU G 482 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR G 486 " --> pdb=" O LEU G 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 482 through 486' Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 42 Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AA3, first strand: chain 'C' and resid 86 through 88 removed outlier: 4.362A pdb=" N VAL C 244 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 96 removed outlier: 4.018A pdb=" N GLU C 93 " --> pdb=" O CYS C 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.187A pdb=" N LEU C 262 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 443 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY C 451 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU C 292 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU C 453 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU C 290 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR C 455 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL C 288 " --> pdb=" O THR C 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 286 through 300 current: chain 'C' and resid 359 through 361 Processing sheet with id=AA8, first strand: chain 'C' and resid 274 through 276 removed outlier: 11.112A pdb=" N VAL C 288 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR C 455 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU C 290 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU C 453 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU C 292 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY C 451 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 443 " --> pdb=" O ARG C 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 413 through 421 removed outlier: 4.239A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 310 removed outlier: 6.035A pdb=" N THR C 305 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'E' and resid 37 through 42 Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 58 Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 88 removed outlier: 4.361A pdb=" N VAL E 244 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 93 through 96 removed outlier: 4.019A pdb=" N GLU E 93 " --> pdb=" O CYS E 241 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB7, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.188A pdb=" N LEU E 262 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 443 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY E 451 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU E 292 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU E 453 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU E 290 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N THR E 455 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL E 288 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 286 through 300 current: chain 'E' and resid 359 through 361 Processing sheet with id=AB9, first strand: chain 'E' and resid 274 through 276 removed outlier: 11.112A pdb=" N VAL E 288 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N THR E 455 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU E 290 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU E 453 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU E 292 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY E 451 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 443 " --> pdb=" O ARG E 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 421 removed outlier: 4.240A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 310 removed outlier: 6.035A pdb=" N THR E 305 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 42 Processing sheet with id=AC4, first strand: chain 'G' and resid 57 through 58 Processing sheet with id=AC5, first strand: chain 'G' and resid 86 through 88 removed outlier: 4.361A pdb=" N VAL G 244 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 93 through 96 removed outlier: 4.018A pdb=" N GLU G 93 " --> pdb=" O CYS G 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 156 through 159 Processing sheet with id=AC8, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AC9, first strand: chain 'G' and resid 262 through 263 removed outlier: 6.187A pdb=" N LEU G 262 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 443 " --> pdb=" O ARG G 300 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY G 451 " --> pdb=" O GLU G 292 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU G 292 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU G 453 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU G 290 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR G 455 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL G 288 " --> pdb=" O THR G 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 286 through 300 current: chain 'G' and resid 359 through 361 Processing sheet with id=AD1, first strand: chain 'G' and resid 274 through 276 removed outlier: 11.112A pdb=" N VAL G 288 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR G 455 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU G 290 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU G 453 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU G 292 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY G 451 " --> pdb=" O GLU G 292 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 443 " --> pdb=" O ARG G 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 413 through 421 removed outlier: 4.240A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS G 385 " --> pdb=" O HIS G 374 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 304 through 310 removed outlier: 6.035A pdb=" N THR G 305 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 423 through 424 424 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2202 1.30 - 1.43: 3362 1.43 - 1.56: 7876 1.56 - 1.69: 6 1.69 - 1.82: 144 Bond restraints: 13590 Sorted by residual: bond pdb=" C GLN C 315 " pdb=" O GLN C 315 " ideal model delta sigma weight residual 1.235 1.166 0.070 1.28e-02 6.10e+03 2.96e+01 bond pdb=" CA ILE C 311 " pdb=" CB ILE C 311 " ideal model delta sigma weight residual 1.540 1.488 0.052 1.36e-02 5.41e+03 1.48e+01 bond pdb=" N ARG C 310 " pdb=" CA ARG C 310 " ideal model delta sigma weight residual 1.453 1.410 0.044 1.22e-02 6.72e+03 1.29e+01 bond pdb=" CB ILE C 311 " pdb=" CG1 ILE C 311 " ideal model delta sigma weight residual 1.530 1.459 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N ILE C 311 " pdb=" CA ILE C 311 " ideal model delta sigma weight residual 1.459 1.417 0.042 1.25e-02 6.40e+03 1.13e+01 ... (remaining 13585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 17897 2.39 - 4.77: 471 4.77 - 7.16: 61 7.16 - 9.54: 8 9.54 - 11.93: 4 Bond angle restraints: 18441 Sorted by residual: angle pdb=" N THR G 163 " pdb=" CA THR G 163 " pdb=" C THR G 163 " ideal model delta sigma weight residual 109.24 118.85 -9.61 1.63e+00 3.76e-01 3.48e+01 angle pdb=" N THR C 163 " pdb=" CA THR C 163 " pdb=" C THR C 163 " ideal model delta sigma weight residual 109.24 118.84 -9.60 1.63e+00 3.76e-01 3.47e+01 angle pdb=" N THR E 163 " pdb=" CA THR E 163 " pdb=" C THR E 163 " ideal model delta sigma weight residual 109.24 118.82 -9.58 1.63e+00 3.76e-01 3.45e+01 angle pdb=" N ILE C 311 " pdb=" CA ILE C 311 " pdb=" C ILE C 311 " ideal model delta sigma weight residual 109.34 97.41 11.93 2.08e+00 2.31e-01 3.29e+01 angle pdb=" C GLY C 312 " pdb=" N PRO C 313 " pdb=" CA PRO C 313 " ideal model delta sigma weight residual 119.84 126.69 -6.85 1.25e+00 6.40e-01 3.00e+01 ... (remaining 18436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 7627 25.09 - 50.18: 714 50.18 - 75.27: 114 75.27 - 100.36: 51 100.36 - 125.45: 38 Dihedral angle restraints: 8544 sinusoidal: 3780 harmonic: 4764 Sorted by residual: dihedral pdb=" CB CYS C 230 " pdb=" SG CYS C 230 " pdb=" SG CYS C 241 " pdb=" CB CYS C 241 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS G 230 " pdb=" SG CYS G 230 " pdb=" SG CYS G 241 " pdb=" CB CYS G 241 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS E 230 " pdb=" SG CYS E 230 " pdb=" SG CYS E 241 " pdb=" CB CYS E 241 " ideal model delta sinusoidal sigma weight residual 93.00 168.73 -75.73 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1780 0.067 - 0.135: 333 0.135 - 0.202: 28 0.202 - 0.269: 3 0.269 - 0.336: 1 Chirality restraints: 2145 Sorted by residual: chirality pdb=" CA ILE C 311 " pdb=" N ILE C 311 " pdb=" C ILE C 311 " pdb=" CB ILE C 311 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ILE E 311 " pdb=" N ILE E 311 " pdb=" C ILE E 311 " pdb=" CB ILE E 311 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE G 311 " pdb=" N ILE G 311 " pdb=" C ILE G 311 " pdb=" CB ILE G 311 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2142 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 604 " 0.360 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG G 604 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG G 604 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG G 604 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG G 604 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " 0.360 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG C 604 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " 0.360 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG E 604 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " 0.123 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 66 2.45 - 3.06: 8768 3.06 - 3.67: 19308 3.67 - 4.29: 27190 4.29 - 4.90: 45239 Nonbonded interactions: 100571 Sorted by model distance: nonbonded pdb=" CG PRO C 329 " pdb=" O CYS C 418 " model vdw 1.835 3.440 nonbonded pdb=" CG PRO G 329 " pdb=" O CYS G 418 " model vdw 1.874 3.440 nonbonded pdb=" CG PRO E 329 " pdb=" O CYS E 418 " model vdw 1.981 3.440 nonbonded pdb=" O ILE G 311 " pdb=" CB GLN G 315 " model vdw 2.095 3.440 nonbonded pdb=" OG1 THR A 606 " pdb=" O VAL C 38 " model vdw 2.114 3.040 ... (remaining 100566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 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: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.660 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.006 0.121 13644 Z= 0.299 Angle : 0.895 11.931 18567 Z= 0.485 Chirality : 0.051 0.336 2145 Planarity : 0.013 0.307 2325 Dihedral : 21.491 125.448 5334 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.42 % Favored : 88.95 % Rotamer: Outliers : 1.36 % Allowed : 29.13 % Favored : 69.51 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -2.43 (0.20), residues: 1593 helix: 0.05 (0.27), residues: 381 sheet: -1.28 (0.24), residues: 396 loop : -2.68 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 610 HIS 0.004 0.001 HIS C 251 PHE 0.022 0.003 PHE C 161 TYR 0.016 0.002 TYR G 484 ARG 0.008 0.001 ARG G 306 Details of bonding type rmsd link_NAG-ASN : bond 0.01024 ( 15) link_NAG-ASN : angle 3.01647 ( 45) hydrogen bonds : bond 0.19636 ( 403) hydrogen bonds : angle 6.73139 ( 1173) link_BETA1-6 : bond 0.00207 ( 3) link_BETA1-6 : angle 0.91290 ( 9) SS BOND : bond 0.02077 ( 36) SS BOND : angle 1.87363 ( 72) covalent geometry : bond 0.00635 (13590) covalent geometry : angle 0.87799 (18441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 354 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 592 LEU cc_start: 0.9079 (mt) cc_final: 0.8811 (mm) REVERT: D 591 GLN cc_start: 0.8450 (tp40) cc_final: 0.8221 (tp-100) REVERT: G 118 LEU cc_start: 0.8402 (tp) cc_final: 0.8049 (tp) outliers start: 20 outliers final: 4 residues processed: 370 average time/residue: 0.3076 time to fit residues: 156.0902 Evaluate side-chains 191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 653 GLN B 611 ASN B 616 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 205 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 205 GLN G 105 GLN G 205 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.047798 restraints weight = 74315.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049496 restraints weight = 42069.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050715 restraints weight = 28270.180| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13644 Z= 0.176 Angle : 0.823 9.548 18567 Z= 0.405 Chirality : 0.051 0.266 2145 Planarity : 0.005 0.051 2325 Dihedral : 16.798 118.236 2169 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.16 % Favored : 91.46 % Rotamer: Outliers : 1.02 % Allowed : 5.49 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.25 (0.20), residues: 1593 helix: 0.25 (0.27), residues: 384 sheet: -1.29 (0.23), residues: 438 loop : -2.58 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 47 HIS 0.004 0.001 HIS C 218 PHE 0.020 0.002 PHE D 573 TYR 0.045 0.002 TYR D 643 ARG 0.005 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 15) link_NAG-ASN : angle 3.16928 ( 45) hydrogen bonds : bond 0.04779 ( 403) hydrogen bonds : angle 5.57572 ( 1173) link_BETA1-6 : bond 0.00277 ( 3) link_BETA1-6 : angle 1.83632 ( 9) SS BOND : bond 0.00957 ( 36) SS BOND : angle 1.48109 ( 72) covalent geometry : bond 0.00402 (13590) covalent geometry : angle 0.80405 (18441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 293 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 530 MET cc_start: 0.8811 (mmm) cc_final: 0.7944 (mmm) REVERT: A 539 VAL cc_start: 0.8797 (t) cc_final: 0.8521 (p) REVERT: A 629 MET cc_start: 0.9481 (mmm) cc_final: 0.8801 (mmm) REVERT: B 530 MET cc_start: 0.8632 (mmt) cc_final: 0.7854 (mmm) REVERT: C 102 MET cc_start: 0.9372 (mtm) cc_final: 0.9150 (mpp) REVERT: C 113 LEU cc_start: 0.9408 (mt) cc_final: 0.9174 (mt) REVERT: C 118 LEU cc_start: 0.9483 (tp) cc_final: 0.9234 (pp) REVERT: C 261 LEU cc_start: 0.9498 (mt) cc_final: 0.9280 (mt) REVERT: D 530 MET cc_start: 0.9210 (tpp) cc_final: 0.8998 (mmm) REVERT: D 601 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7452 (ptpp) REVERT: D 611 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.7091 (p0) REVERT: D 626 MET cc_start: 0.8986 (tpt) cc_final: 0.8564 (tpt) REVERT: E 209 LYS cc_start: 0.9237 (mppt) cc_final: 0.8973 (tptt) REVERT: E 261 LEU cc_start: 0.9550 (mt) cc_final: 0.9315 (mt) REVERT: G 40 VAL cc_start: 0.9515 (t) cc_final: 0.9185 (p) REVERT: G 88 LEU cc_start: 0.9451 (mt) cc_final: 0.8959 (mp) REVERT: G 100 ASN cc_start: 0.8781 (t0) cc_final: 0.7782 (t0) REVERT: G 102 MET cc_start: 0.9256 (mtm) cc_final: 0.9036 (mtm) REVERT: G 261 LEU cc_start: 0.9510 (mt) cc_final: 0.9307 (mt) REVERT: G 315 GLN cc_start: 0.9557 (mp10) cc_final: 0.9236 (mp10) REVERT: G 434 MET cc_start: 0.9293 (mtm) cc_final: 0.9082 (mpp) outliers start: 15 outliers final: 6 residues processed: 304 average time/residue: 0.2886 time to fit residues: 122.7309 Evaluate side-chains 191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 352 HIS G 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047376 restraints weight = 76396.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049079 restraints weight = 43350.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050302 restraints weight = 29205.959| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13644 Z= 0.147 Angle : 0.740 9.383 18567 Z= 0.363 Chirality : 0.048 0.275 2145 Planarity : 0.004 0.058 2325 Dihedral : 13.453 112.295 2169 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.85 % Favored : 90.77 % Rotamer: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.20), residues: 1593 helix: 0.15 (0.26), residues: 387 sheet: -1.19 (0.23), residues: 435 loop : -2.45 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 571 HIS 0.004 0.001 HIS C 218 PHE 0.014 0.002 PHE D 573 TYR 0.013 0.001 TYR B 643 ARG 0.007 0.001 ARG A 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 15) link_NAG-ASN : angle 2.53945 ( 45) hydrogen bonds : bond 0.04360 ( 403) hydrogen bonds : angle 5.25524 ( 1173) link_BETA1-6 : bond 0.00250 ( 3) link_BETA1-6 : angle 1.74277 ( 9) SS BOND : bond 0.00276 ( 36) SS BOND : angle 0.98968 ( 72) covalent geometry : bond 0.00342 (13590) covalent geometry : angle 0.72802 (18441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8860 (mmm) cc_final: 0.8198 (mmm) REVERT: A 537 LEU cc_start: 0.9322 (mt) cc_final: 0.9029 (mp) REVERT: A 598 CYS cc_start: 0.8128 (m) cc_final: 0.7802 (m) REVERT: A 629 MET cc_start: 0.9440 (mmm) cc_final: 0.9068 (mmm) REVERT: B 530 MET cc_start: 0.8713 (mmt) cc_final: 0.8003 (mmm) REVERT: B 577 GLN cc_start: 0.8961 (mt0) cc_final: 0.8680 (mt0) REVERT: B 581 LEU cc_start: 0.9640 (mm) cc_final: 0.9363 (mm) REVERT: B 629 MET cc_start: 0.9604 (mmt) cc_final: 0.9325 (mmt) REVERT: D 537 LEU cc_start: 0.8760 (mt) cc_final: 0.8428 (mp) REVERT: D 624 ASP cc_start: 0.9523 (m-30) cc_final: 0.9295 (m-30) REVERT: D 626 MET cc_start: 0.8961 (tpt) cc_final: 0.8552 (tpt) REVERT: D 643 TYR cc_start: 0.9651 (m-80) cc_final: 0.9426 (m-80) REVERT: D 645 LEU cc_start: 0.9739 (mt) cc_final: 0.9517 (pp) REVERT: E 102 MET cc_start: 0.9158 (mtm) cc_final: 0.8923 (mtm) REVERT: E 118 LEU cc_start: 0.9582 (tp) cc_final: 0.9351 (pp) REVERT: E 209 LYS cc_start: 0.9220 (mppt) cc_final: 0.8996 (tptt) REVERT: G 102 MET cc_start: 0.9237 (mtm) cc_final: 0.8698 (mpp) REVERT: G 434 MET cc_start: 0.9211 (mtm) cc_final: 0.8922 (mpp) outliers start: 1 outliers final: 1 residues processed: 266 average time/residue: 0.2830 time to fit residues: 105.5244 Evaluate side-chains 190 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 94 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045341 restraints weight = 77962.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046940 restraints weight = 44446.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048057 restraints weight = 30199.210| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13644 Z= 0.182 Angle : 0.741 9.570 18567 Z= 0.363 Chirality : 0.047 0.260 2145 Planarity : 0.004 0.034 2325 Dihedral : 10.591 77.244 2169 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.23 % Favored : 90.40 % Rotamer: Outliers : 0.14 % Allowed : 5.08 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.20), residues: 1593 helix: 0.15 (0.26), residues: 387 sheet: -1.04 (0.23), residues: 423 loop : -2.44 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 571 HIS 0.004 0.001 HIS E 251 PHE 0.025 0.002 PHE D 573 TYR 0.009 0.001 TYR C 486 ARG 0.009 0.001 ARG D 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 15) link_NAG-ASN : angle 2.79885 ( 45) hydrogen bonds : bond 0.04167 ( 403) hydrogen bonds : angle 5.17848 ( 1173) link_BETA1-6 : bond 0.00044 ( 3) link_BETA1-6 : angle 1.59863 ( 9) SS BOND : bond 0.00323 ( 36) SS BOND : angle 0.99420 ( 72) covalent geometry : bond 0.00405 (13590) covalent geometry : angle 0.72679 (18441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9056 (mmm) cc_final: 0.8656 (mmm) REVERT: A 537 LEU cc_start: 0.9358 (mt) cc_final: 0.9070 (mp) REVERT: A 598 CYS cc_start: 0.8088 (m) cc_final: 0.7719 (m) REVERT: A 629 MET cc_start: 0.9403 (mmm) cc_final: 0.8904 (mmm) REVERT: B 530 MET cc_start: 0.8846 (mmt) cc_final: 0.8065 (mmm) REVERT: B 643 TYR cc_start: 0.9734 (m-80) cc_final: 0.9531 (m-80) REVERT: C 434 MET cc_start: 0.9144 (mtm) cc_final: 0.8378 (mpp) REVERT: D 537 LEU cc_start: 0.8878 (mt) cc_final: 0.8552 (mp) REVERT: D 601 LYS cc_start: 0.8358 (mtpt) cc_final: 0.7734 (ptmt) REVERT: D 624 ASP cc_start: 0.9544 (m-30) cc_final: 0.9313 (m-30) REVERT: D 626 MET cc_start: 0.9196 (tpt) cc_final: 0.8952 (tpt) REVERT: E 102 MET cc_start: 0.9118 (mtm) cc_final: 0.8528 (mpp) REVERT: E 118 LEU cc_start: 0.9576 (tp) cc_final: 0.9350 (pp) REVERT: E 123 LYS cc_start: 0.8441 (tptp) cc_final: 0.8206 (tptp) REVERT: E 434 MET cc_start: 0.8833 (mpp) cc_final: 0.8496 (mpp) REVERT: G 70 VAL cc_start: 0.9573 (m) cc_final: 0.9173 (p) REVERT: G 88 LEU cc_start: 0.9349 (mp) cc_final: 0.9009 (mp) REVERT: G 102 MET cc_start: 0.9288 (mtm) cc_final: 0.8812 (mpp) REVERT: G 261 LEU cc_start: 0.9500 (mt) cc_final: 0.9267 (mt) REVERT: G 434 MET cc_start: 0.9305 (mtm) cc_final: 0.9081 (mpp) outliers start: 2 outliers final: 1 residues processed: 228 average time/residue: 0.2835 time to fit residues: 90.4466 Evaluate side-chains 157 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.045190 restraints weight = 79394.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046819 restraints weight = 44764.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047989 restraints weight = 30051.032| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13644 Z= 0.159 Angle : 0.715 9.419 18567 Z= 0.352 Chirality : 0.047 0.265 2145 Planarity : 0.004 0.035 2325 Dihedral : 9.658 73.091 2169 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.47 % Favored : 91.15 % Rotamer: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1593 helix: 0.33 (0.26), residues: 390 sheet: -0.84 (0.24), residues: 420 loop : -2.32 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 571 HIS 0.003 0.001 HIS C 74 PHE 0.023 0.002 PHE D 573 TYR 0.023 0.001 TYR D 643 ARG 0.008 0.001 ARG A 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 15) link_NAG-ASN : angle 2.74542 ( 45) hydrogen bonds : bond 0.03932 ( 403) hydrogen bonds : angle 5.05025 ( 1173) link_BETA1-6 : bond 0.00101 ( 3) link_BETA1-6 : angle 1.60761 ( 9) SS BOND : bond 0.00301 ( 36) SS BOND : angle 1.05140 ( 72) covalent geometry : bond 0.00360 (13590) covalent geometry : angle 0.70088 (18441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9107 (mmm) cc_final: 0.8699 (mmm) REVERT: A 537 LEU cc_start: 0.9389 (mt) cc_final: 0.9124 (mp) REVERT: A 598 CYS cc_start: 0.8067 (m) cc_final: 0.7673 (m) REVERT: A 629 MET cc_start: 0.9416 (mmm) cc_final: 0.8917 (mmm) REVERT: B 530 MET cc_start: 0.8930 (mmt) cc_final: 0.8279 (mmm) REVERT: C 70 VAL cc_start: 0.9389 (m) cc_final: 0.8881 (p) REVERT: C 108 GLU cc_start: 0.9460 (pm20) cc_final: 0.9185 (pm20) REVERT: C 115 ASP cc_start: 0.9313 (t0) cc_final: 0.9083 (t0) REVERT: C 118 LEU cc_start: 0.9597 (tp) cc_final: 0.9257 (pp) REVERT: C 434 MET cc_start: 0.9074 (mtm) cc_final: 0.8543 (mpp) REVERT: D 537 LEU cc_start: 0.8927 (mt) cc_final: 0.8617 (mp) REVERT: D 624 ASP cc_start: 0.9526 (m-30) cc_final: 0.9289 (m-30) REVERT: D 626 MET cc_start: 0.9127 (tpt) cc_final: 0.8686 (tpp) REVERT: D 643 TYR cc_start: 0.9616 (m-80) cc_final: 0.8894 (m-80) REVERT: E 40 VAL cc_start: 0.9477 (t) cc_final: 0.9184 (p) REVERT: E 88 LEU cc_start: 0.9442 (mp) cc_final: 0.9241 (mp) REVERT: E 102 MET cc_start: 0.9124 (mtm) cc_final: 0.8731 (mtm) REVERT: E 118 LEU cc_start: 0.9565 (tp) cc_final: 0.9362 (pp) REVERT: E 434 MET cc_start: 0.8878 (mpp) cc_final: 0.8563 (mpp) REVERT: G 70 VAL cc_start: 0.9369 (m) cc_final: 0.8915 (p) REVERT: G 88 LEU cc_start: 0.9339 (mp) cc_final: 0.9002 (mp) REVERT: G 102 MET cc_start: 0.9311 (mtm) cc_final: 0.8833 (mpp) REVERT: G 434 MET cc_start: 0.9243 (mtm) cc_final: 0.8951 (mpp) outliers start: 2 outliers final: 1 residues processed: 231 average time/residue: 0.3372 time to fit residues: 109.7838 Evaluate side-chains 156 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 142 optimal weight: 0.0770 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN C 422 GLN D 650 GLN D 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045502 restraints weight = 78695.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047138 restraints weight = 44100.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048334 restraints weight = 29679.565| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13644 Z= 0.128 Angle : 0.706 9.512 18567 Z= 0.345 Chirality : 0.047 0.257 2145 Planarity : 0.004 0.036 2325 Dihedral : 9.265 70.216 2169 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.16 % Favored : 91.46 % Rotamer: Outliers : 0.20 % Allowed : 3.32 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1593 helix: 0.32 (0.26), residues: 390 sheet: -0.60 (0.26), residues: 390 loop : -2.30 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 571 HIS 0.002 0.001 HIS E 352 PHE 0.017 0.001 PHE D 573 TYR 0.027 0.001 TYR A 643 ARG 0.010 0.001 ARG D 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 15) link_NAG-ASN : angle 2.57651 ( 45) hydrogen bonds : bond 0.03770 ( 403) hydrogen bonds : angle 4.99040 ( 1173) link_BETA1-6 : bond 0.00176 ( 3) link_BETA1-6 : angle 1.62383 ( 9) SS BOND : bond 0.00193 ( 36) SS BOND : angle 1.04366 ( 72) covalent geometry : bond 0.00298 (13590) covalent geometry : angle 0.69287 (18441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 530 MET cc_start: 0.9212 (mmm) cc_final: 0.8805 (mmm) REVERT: A 537 LEU cc_start: 0.9353 (mt) cc_final: 0.9079 (mp) REVERT: A 598 CYS cc_start: 0.8069 (m) cc_final: 0.7651 (m) REVERT: A 643 TYR cc_start: 0.9691 (m-80) cc_final: 0.9412 (m-80) REVERT: B 530 MET cc_start: 0.8981 (mmt) cc_final: 0.8320 (mmm) REVERT: B 632 ASP cc_start: 0.9812 (t70) cc_final: 0.9580 (p0) REVERT: C 70 VAL cc_start: 0.9379 (m) cc_final: 0.8973 (p) REVERT: C 100 ASN cc_start: 0.8744 (t0) cc_final: 0.7866 (t0) REVERT: C 115 ASP cc_start: 0.9292 (t0) cc_final: 0.9037 (t0) REVERT: C 118 LEU cc_start: 0.9539 (tp) cc_final: 0.9216 (pp) REVERT: C 434 MET cc_start: 0.9147 (mtm) cc_final: 0.8624 (mpp) REVERT: D 537 LEU cc_start: 0.8882 (mt) cc_final: 0.8560 (mp) REVERT: D 624 ASP cc_start: 0.9548 (m-30) cc_final: 0.9303 (m-30) REVERT: D 626 MET cc_start: 0.9157 (tpt) cc_final: 0.8680 (tpp) REVERT: E 70 VAL cc_start: 0.9303 (m) cc_final: 0.8789 (p) REVERT: E 102 MET cc_start: 0.9116 (mtm) cc_final: 0.8709 (mtm) REVERT: E 118 LEU cc_start: 0.9544 (tp) cc_final: 0.9343 (pp) REVERT: E 196 ILE cc_start: 0.9135 (mm) cc_final: 0.8835 (mm) REVERT: G 70 VAL cc_start: 0.9347 (m) cc_final: 0.8912 (p) REVERT: G 88 LEU cc_start: 0.9295 (mp) cc_final: 0.8966 (mp) REVERT: G 100 ASN cc_start: 0.8728 (t0) cc_final: 0.8032 (t0) REVERT: G 102 MET cc_start: 0.9341 (mtm) cc_final: 0.9129 (mtt) REVERT: G 434 MET cc_start: 0.9216 (mtm) cc_final: 0.8877 (mpp) outliers start: 3 outliers final: 1 residues processed: 227 average time/residue: 0.3657 time to fit residues: 117.6333 Evaluate side-chains 160 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN B 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.055499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.044526 restraints weight = 80748.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.046077 restraints weight = 45854.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047191 restraints weight = 31058.064| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13644 Z= 0.188 Angle : 0.733 9.458 18567 Z= 0.361 Chirality : 0.047 0.267 2145 Planarity : 0.004 0.035 2325 Dihedral : 8.980 68.013 2169 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.91 % Favored : 90.71 % Rotamer: Outliers : 0.20 % Allowed : 2.17 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.20), residues: 1593 helix: 0.40 (0.26), residues: 393 sheet: -0.58 (0.26), residues: 390 loop : -2.32 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 610 HIS 0.003 0.001 HIS C 251 PHE 0.015 0.002 PHE D 573 TYR 0.020 0.002 TYR A 643 ARG 0.011 0.001 ARG D 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 15) link_NAG-ASN : angle 2.84707 ( 45) hydrogen bonds : bond 0.03949 ( 403) hydrogen bonds : angle 5.03757 ( 1173) link_BETA1-6 : bond 0.00175 ( 3) link_BETA1-6 : angle 1.54264 ( 9) SS BOND : bond 0.00307 ( 36) SS BOND : angle 1.31361 ( 72) covalent geometry : bond 0.00409 (13590) covalent geometry : angle 0.71638 (18441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 530 MET cc_start: 0.9288 (mmm) cc_final: 0.8910 (mmm) REVERT: A 537 LEU cc_start: 0.9408 (mt) cc_final: 0.9139 (mp) REVERT: A 629 MET cc_start: 0.9369 (mmm) cc_final: 0.8872 (mmm) REVERT: B 530 MET cc_start: 0.9125 (mmt) cc_final: 0.8473 (mmm) REVERT: B 643 TYR cc_start: 0.9644 (m-80) cc_final: 0.9398 (m-80) REVERT: C 70 VAL cc_start: 0.9457 (m) cc_final: 0.9062 (p) REVERT: C 115 ASP cc_start: 0.9367 (t0) cc_final: 0.9048 (t0) REVERT: C 118 LEU cc_start: 0.9584 (tp) cc_final: 0.9234 (pp) REVERT: C 261 LEU cc_start: 0.9417 (mt) cc_final: 0.9198 (mt) REVERT: C 434 MET cc_start: 0.9139 (mtm) cc_final: 0.8619 (mpp) REVERT: D 537 LEU cc_start: 0.8972 (mt) cc_final: 0.8646 (mp) REVERT: D 611 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7177 (p0) REVERT: D 624 ASP cc_start: 0.9537 (m-30) cc_final: 0.9288 (m-30) REVERT: D 626 MET cc_start: 0.9096 (tpt) cc_final: 0.8597 (tpp) REVERT: D 643 TYR cc_start: 0.9598 (m-80) cc_final: 0.8907 (m-80) REVERT: E 70 VAL cc_start: 0.9415 (m) cc_final: 0.9011 (p) REVERT: E 102 MET cc_start: 0.9097 (mtm) cc_final: 0.8714 (mtm) REVERT: E 118 LEU cc_start: 0.9583 (tp) cc_final: 0.9369 (pp) REVERT: E 123 LYS cc_start: 0.8810 (tptp) cc_final: 0.8516 (tptt) REVERT: E 261 LEU cc_start: 0.9426 (mt) cc_final: 0.9208 (mt) REVERT: G 70 VAL cc_start: 0.9446 (m) cc_final: 0.9033 (p) REVERT: G 88 LEU cc_start: 0.9317 (mp) cc_final: 0.9040 (mp) REVERT: G 102 MET cc_start: 0.9314 (mtm) cc_final: 0.8794 (mtt) REVERT: G 108 GLU cc_start: 0.9356 (pp20) cc_final: 0.8832 (pp20) REVERT: G 434 MET cc_start: 0.9289 (mtm) cc_final: 0.8859 (mpp) outliers start: 3 outliers final: 1 residues processed: 206 average time/residue: 0.3564 time to fit residues: 103.0380 Evaluate side-chains 155 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 113 optimal weight: 0.0170 chunk 156 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 0.0040 overall best weight: 1.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 616 ASN B 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN D 652 GLN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044853 restraints weight = 80051.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.046429 restraints weight = 45568.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047536 restraints weight = 31065.817| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13644 Z= 0.137 Angle : 0.719 9.393 18567 Z= 0.354 Chirality : 0.047 0.254 2145 Planarity : 0.004 0.042 2325 Dihedral : 8.690 64.753 2169 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.22 % Favored : 91.40 % Rotamer: Outliers : 0.20 % Allowed : 1.63 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1593 helix: 0.33 (0.26), residues: 393 sheet: -0.74 (0.25), residues: 420 loop : -2.12 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 610 HIS 0.002 0.001 HIS G 251 PHE 0.020 0.001 PHE D 573 TYR 0.007 0.001 TYR E 225 ARG 0.009 0.001 ARG E 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 15) link_NAG-ASN : angle 2.91717 ( 45) hydrogen bonds : bond 0.03877 ( 403) hydrogen bonds : angle 5.04666 ( 1173) link_BETA1-6 : bond 0.00343 ( 3) link_BETA1-6 : angle 1.65246 ( 9) SS BOND : bond 0.00240 ( 36) SS BOND : angle 1.17305 ( 72) covalent geometry : bond 0.00314 (13590) covalent geometry : angle 0.70258 (18441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9317 (mmm) cc_final: 0.8865 (mmm) REVERT: A 537 LEU cc_start: 0.9408 (mt) cc_final: 0.9150 (mp) REVERT: A 629 MET cc_start: 0.9398 (mmm) cc_final: 0.8923 (mmm) REVERT: A 643 TYR cc_start: 0.9702 (m-80) cc_final: 0.8909 (m-80) REVERT: B 530 MET cc_start: 0.9200 (mmt) cc_final: 0.8553 (mmm) REVERT: B 659 ASP cc_start: 0.7547 (p0) cc_final: 0.7341 (p0) REVERT: C 70 VAL cc_start: 0.9458 (m) cc_final: 0.8945 (p) REVERT: C 102 MET cc_start: 0.9373 (mtm) cc_final: 0.8991 (mtm) REVERT: C 114 TRP cc_start: 0.9510 (m100) cc_final: 0.9235 (t-100) REVERT: C 115 ASP cc_start: 0.9375 (t0) cc_final: 0.9092 (t0) REVERT: C 118 LEU cc_start: 0.9530 (tp) cc_final: 0.9316 (pp) REVERT: C 261 LEU cc_start: 0.9430 (mt) cc_final: 0.9194 (mt) REVERT: C 304 MET cc_start: 0.8893 (mmm) cc_final: 0.8230 (mmp) REVERT: C 434 MET cc_start: 0.8764 (mpp) cc_final: 0.7973 (mpp) REVERT: D 537 LEU cc_start: 0.8945 (mt) cc_final: 0.8629 (mp) REVERT: D 611 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7204 (p0) REVERT: D 624 ASP cc_start: 0.9556 (m-30) cc_final: 0.9302 (m-30) REVERT: D 626 MET cc_start: 0.9156 (tpt) cc_final: 0.8822 (tpp) REVERT: D 643 TYR cc_start: 0.9609 (m-80) cc_final: 0.8914 (m-80) REVERT: E 70 VAL cc_start: 0.9191 (m) cc_final: 0.8689 (p) REVERT: E 102 MET cc_start: 0.9083 (mtm) cc_final: 0.8717 (mtm) REVERT: E 109 ASP cc_start: 0.9507 (m-30) cc_final: 0.9147 (m-30) REVERT: E 118 LEU cc_start: 0.9567 (tp) cc_final: 0.9362 (pp) REVERT: E 261 LEU cc_start: 0.9436 (mt) cc_final: 0.9220 (mt) REVERT: G 70 VAL cc_start: 0.9441 (m) cc_final: 0.9010 (p) REVERT: G 102 MET cc_start: 0.9303 (mtm) cc_final: 0.8758 (mtt) REVERT: G 109 ASP cc_start: 0.9447 (m-30) cc_final: 0.9152 (m-30) REVERT: G 434 MET cc_start: 0.9301 (mtm) cc_final: 0.8835 (mpp) outliers start: 3 outliers final: 0 residues processed: 212 average time/residue: 0.3843 time to fit residues: 116.9484 Evaluate side-chains 155 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 155 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 0.0980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 611 ASN D 577 GLN D 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045422 restraints weight = 77892.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.046982 restraints weight = 44317.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048111 restraints weight = 30322.596| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13644 Z= 0.124 Angle : 0.738 9.869 18567 Z= 0.363 Chirality : 0.048 0.253 2145 Planarity : 0.004 0.042 2325 Dihedral : 8.534 62.929 2169 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.29 % Favored : 91.34 % Rotamer: Outliers : 0.14 % Allowed : 0.68 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1593 helix: 0.21 (0.26), residues: 390 sheet: -0.63 (0.25), residues: 414 loop : -2.11 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 610 HIS 0.003 0.001 HIS E 107 PHE 0.013 0.001 PHE G 212 TYR 0.022 0.001 TYR B 643 ARG 0.012 0.001 ARG B 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 15) link_NAG-ASN : angle 2.92641 ( 45) hydrogen bonds : bond 0.03913 ( 403) hydrogen bonds : angle 5.10978 ( 1173) link_BETA1-6 : bond 0.00248 ( 3) link_BETA1-6 : angle 1.64040 ( 9) SS BOND : bond 0.00203 ( 36) SS BOND : angle 1.04533 ( 72) covalent geometry : bond 0.00282 (13590) covalent geometry : angle 0.72222 (18441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9322 (mmm) cc_final: 0.8868 (mmm) REVERT: A 537 LEU cc_start: 0.9401 (mt) cc_final: 0.9159 (mp) REVERT: A 629 MET cc_start: 0.9376 (mmm) cc_final: 0.9029 (mmm) REVERT: A 633 ARG cc_start: 0.9350 (ptp-110) cc_final: 0.9130 (ptp-110) REVERT: B 633 ARG cc_start: 0.9380 (ptp-110) cc_final: 0.9107 (ptt-90) REVERT: B 643 TYR cc_start: 0.9620 (m-80) cc_final: 0.9412 (m-80) REVERT: B 659 ASP cc_start: 0.7528 (p0) cc_final: 0.7307 (p0) REVERT: C 70 VAL cc_start: 0.9429 (m) cc_final: 0.8906 (p) REVERT: C 102 MET cc_start: 0.9320 (mtm) cc_final: 0.8939 (mtm) REVERT: C 103 VAL cc_start: 0.9487 (m) cc_final: 0.9036 (p) REVERT: C 114 TRP cc_start: 0.9505 (m100) cc_final: 0.9235 (t-100) REVERT: C 261 LEU cc_start: 0.9436 (mt) cc_final: 0.9204 (mt) REVERT: C 304 MET cc_start: 0.8913 (mmm) cc_final: 0.8225 (mmp) REVERT: C 434 MET cc_start: 0.8738 (mpp) cc_final: 0.7870 (mpp) REVERT: D 624 ASP cc_start: 0.9532 (m-30) cc_final: 0.9272 (m-30) REVERT: D 626 MET cc_start: 0.9079 (tpt) cc_final: 0.8741 (tpp) REVERT: E 70 VAL cc_start: 0.9230 (m) cc_final: 0.8818 (p) REVERT: E 102 MET cc_start: 0.9011 (mtm) cc_final: 0.8674 (mtm) REVERT: E 261 LEU cc_start: 0.9443 (mt) cc_final: 0.9236 (mt) REVERT: G 70 VAL cc_start: 0.9352 (m) cc_final: 0.8889 (p) REVERT: G 100 ASN cc_start: 0.8742 (t0) cc_final: 0.7954 (t0) REVERT: G 102 MET cc_start: 0.9245 (mtm) cc_final: 0.9045 (mtt) REVERT: G 109 ASP cc_start: 0.9657 (m-30) cc_final: 0.9424 (m-30) REVERT: G 434 MET cc_start: 0.9270 (mtm) cc_final: 0.8815 (mpp) REVERT: G 492 LYS cc_start: 0.9558 (mttt) cc_final: 0.9340 (mtmm) outliers start: 2 outliers final: 2 residues processed: 214 average time/residue: 0.3051 time to fit residues: 91.5585 Evaluate side-chains 158 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.055117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.044099 restraints weight = 80268.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045627 restraints weight = 45311.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046742 restraints weight = 30738.770| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13644 Z= 0.170 Angle : 0.758 9.333 18567 Z= 0.372 Chirality : 0.048 0.265 2145 Planarity : 0.004 0.056 2325 Dihedral : 8.378 61.778 2169 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.85 % Favored : 91.71 % Rotamer: Outliers : 0.20 % Allowed : 0.47 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1593 helix: 0.27 (0.27), residues: 390 sheet: -0.63 (0.25), residues: 414 loop : -2.03 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 47 HIS 0.003 0.001 HIS E 251 PHE 0.012 0.001 PHE E 212 TYR 0.025 0.001 TYR A 643 ARG 0.018 0.001 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 15) link_NAG-ASN : angle 3.08698 ( 45) hydrogen bonds : bond 0.04026 ( 403) hydrogen bonds : angle 5.19174 ( 1173) link_BETA1-6 : bond 0.00163 ( 3) link_BETA1-6 : angle 1.60824 ( 9) SS BOND : bond 0.00292 ( 36) SS BOND : angle 1.14529 ( 72) covalent geometry : bond 0.00377 (13590) covalent geometry : angle 0.74091 (18441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9381 (mmm) cc_final: 0.8872 (mmm) REVERT: A 629 MET cc_start: 0.9412 (mmm) cc_final: 0.9101 (mmm) REVERT: A 633 ARG cc_start: 0.9352 (ptp-110) cc_final: 0.9132 (ptp-110) REVERT: A 643 TYR cc_start: 0.9683 (m-80) cc_final: 0.8986 (m-80) REVERT: B 643 TYR cc_start: 0.9660 (m-80) cc_final: 0.8894 (m-80) REVERT: B 659 ASP cc_start: 0.7540 (p0) cc_final: 0.7316 (p0) REVERT: C 70 VAL cc_start: 0.9517 (m) cc_final: 0.9036 (p) REVERT: C 102 MET cc_start: 0.9359 (mtm) cc_final: 0.8938 (mtm) REVERT: C 103 VAL cc_start: 0.9457 (m) cc_final: 0.9120 (p) REVERT: C 304 MET cc_start: 0.8945 (mmm) cc_final: 0.8303 (mmp) REVERT: C 434 MET cc_start: 0.8794 (mpp) cc_final: 0.7919 (mpp) REVERT: D 624 ASP cc_start: 0.9539 (m-30) cc_final: 0.9229 (m-30) REVERT: D 626 MET cc_start: 0.9054 (tpt) cc_final: 0.8506 (tpp) REVERT: D 640 ASP cc_start: 0.9545 (p0) cc_final: 0.9319 (p0) REVERT: D 643 TYR cc_start: 0.9630 (m-80) cc_final: 0.8935 (m-80) REVERT: E 70 VAL cc_start: 0.9364 (m) cc_final: 0.8950 (p) REVERT: E 102 MET cc_start: 0.8995 (mtm) cc_final: 0.8583 (mtm) REVERT: E 103 VAL cc_start: 0.9468 (m) cc_final: 0.9162 (p) REVERT: G 70 VAL cc_start: 0.9465 (m) cc_final: 0.9026 (p) REVERT: G 100 ASN cc_start: 0.8871 (t0) cc_final: 0.8064 (t0) REVERT: G 102 MET cc_start: 0.9283 (mtm) cc_final: 0.9068 (mtt) REVERT: G 434 MET cc_start: 0.9328 (mtm) cc_final: 0.8862 (mpp) REVERT: G 492 LYS cc_start: 0.9596 (mttt) cc_final: 0.9379 (mtmt) outliers start: 3 outliers final: 2 residues processed: 195 average time/residue: 0.3514 time to fit residues: 96.1737 Evaluate side-chains 151 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 111 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN D 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042692 restraints weight = 82828.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044170 restraints weight = 46733.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.045219 restraints weight = 31747.054| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13644 Z= 0.236 Angle : 0.816 11.995 18567 Z= 0.400 Chirality : 0.048 0.252 2145 Planarity : 0.005 0.045 2325 Dihedral : 8.409 60.361 2169 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 0.20 % Allowed : 0.88 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1593 helix: 0.08 (0.27), residues: 390 sheet: -0.73 (0.25), residues: 414 loop : -2.09 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 610 HIS 0.004 0.001 HIS C 251 PHE 0.013 0.002 PHE C 382 TYR 0.021 0.002 TYR A 643 ARG 0.009 0.001 ARG B 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 15) link_NAG-ASN : angle 3.40202 ( 45) hydrogen bonds : bond 0.04147 ( 403) hydrogen bonds : angle 5.44343 ( 1173) link_BETA1-6 : bond 0.00135 ( 3) link_BETA1-6 : angle 1.69482 ( 9) SS BOND : bond 0.00397 ( 36) SS BOND : angle 1.31530 ( 72) covalent geometry : bond 0.00511 (13590) covalent geometry : angle 0.79630 (18441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4765.54 seconds wall clock time: 87 minutes 11.24 seconds (5231.24 seconds total)