Starting phenix.real_space_refine on Thu Sep 26 14:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/09_2024/8f7t_28910_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/09_2024/8f7t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/09_2024/8f7t_28910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/09_2024/8f7t_28910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/09_2024/8f7t_28910_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/09_2024/8f7t_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-5461/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: 8.59, per 1000 atoms: 0.64 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 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: 1.93 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: 3.65 Time building geometry restraints manager: 3.84 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: 0.00 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.470 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- 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 0.103 13590 Z= 0.410 Angle : 0.878 11.931 18441 Z= 0.481 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 354 time to evaluate : 1.677 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: 0.3006 time to fit residues: 152.3047 Evaluate side-chains 191 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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: 10.0000 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 13590 Z= 0.255 Angle : 0.804 9.548 18441 Z= 0.401 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 293 time to evaluate : 1.788 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: 0.8530 (mmm) cc_final: 0.7660 (mmm) REVERT: A 629 MET cc_start: 0.8645 (mmm) cc_final: 0.7655 (mmm) REVERT: B 530 MET cc_start: 0.8090 (mmt) cc_final: 0.7354 (mmm) REVERT: B 575 GLN cc_start: 0.8270 (pp30) cc_final: 0.7894 (tm-30) REVERT: D 611 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.6671 (p0) REVERT: D 624 ASP cc_start: 0.8623 (m-30) cc_final: 0.8420 (m-30) REVERT: G 40 VAL cc_start: 0.8841 (t) cc_final: 0.8622 (p) REVERT: G 115 ASP cc_start: 0.6810 (t0) cc_final: 0.6596 (t0) outliers start: 15 outliers final: 6 residues processed: 304 average time/residue: 0.2905 time to fit residues: 122.8924 Evaluate side-chains 189 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN D 616 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13590 Z= 0.370 Angle : 0.797 9.421 18441 Z= 0.399 Chirality : 0.049 0.290 2145 Planarity : 0.005 0.041 2325 Dihedral : 13.426 114.969 2169 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.54 % Favored : 90.08 % Rotamer: Outliers : 0.14 % Allowed : 6.37 % 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: -2.37 (0.19), residues: 1593 helix: -0.06 (0.25), residues: 387 sheet: -1.40 (0.22), residues: 432 loop : -2.50 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 571 HIS 0.005 0.001 HIS E 352 PHE 0.016 0.002 PHE G 382 TYR 0.011 0.002 TYR C 318 ARG 0.010 0.001 ARG E 168 *********************** 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 236 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.471 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: A 530 MET cc_start: 0.8727 (mmm) cc_final: 0.7976 (mmm) REVERT: A 629 MET cc_start: 0.8484 (mmm) cc_final: 0.8177 (mmm) REVERT: B 629 MET cc_start: 0.8331 (mmt) cc_final: 0.7884 (mmt) REVERT: C 115 ASP cc_start: 0.7326 (t70) cc_final: 0.7061 (t0) REVERT: D 611 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6673 (p0) REVERT: G 115 ASP cc_start: 0.7158 (t0) cc_final: 0.6821 (t0) outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.2988 time to fit residues: 96.9306 Evaluate side-chains 161 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 611 ASN B 630 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13590 Z= 0.206 Angle : 0.721 9.515 18441 Z= 0.354 Chirality : 0.048 0.279 2145 Planarity : 0.004 0.035 2325 Dihedral : 10.240 75.568 2169 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.10 % Favored : 91.53 % Rotamer: Outliers : 0.20 % Allowed : 4.34 % Favored : 95.46 % 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: 0.03 (0.25), residues: 393 sheet: -1.07 (0.23), residues: 420 loop : -2.47 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 571 HIS 0.003 0.001 HIS C 218 PHE 0.027 0.002 PHE D 573 TYR 0.030 0.002 TYR D 643 ARG 0.007 0.001 ARG A 644 *********************** 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 229 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 1.589 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: A 530 MET cc_start: 0.8847 (mmm) cc_final: 0.8125 (mmm) REVERT: A 629 MET cc_start: 0.8449 (mmm) cc_final: 0.8174 (mmm) REVERT: C 70 VAL cc_start: 0.8122 (m) cc_final: 0.7845 (p) REVERT: D 598 CYS cc_start: 0.5177 (m) cc_final: 0.4861 (m) REVERT: D 601 LYS cc_start: 0.8173 (pttm) cc_final: 0.7941 (pttm) REVERT: G 70 VAL cc_start: 0.8007 (m) cc_final: 0.7771 (p) outliers start: 3 outliers final: 1 residues processed: 229 average time/residue: 0.2973 time to fit residues: 94.0250 Evaluate side-chains 159 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 133 optimal weight: 0.0170 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 overall best weight: 3.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 630 GLN B 611 ASN ** B 650 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13590 Z= 0.304 Angle : 0.736 9.435 18441 Z= 0.366 Chirality : 0.048 0.281 2145 Planarity : 0.004 0.067 2325 Dihedral : 9.460 72.665 2169 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.10 % Favored : 90.52 % Rotamer: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % 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: -2.04 (0.20), residues: 1593 helix: 0.15 (0.25), residues: 396 sheet: -0.90 (0.25), residues: 390 loop : -2.44 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 571 HIS 0.004 0.001 HIS G 251 PHE 0.019 0.002 PHE D 573 TYR 0.011 0.002 TYR G 219 ARG 0.012 0.001 ARG D 633 *********************** 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 196 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.459 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: A 530 MET cc_start: 0.9013 (mmm) cc_final: 0.8367 (mmm) REVERT: A 629 MET cc_start: 0.8575 (mmm) cc_final: 0.8002 (mmm) REVERT: A 643 TYR cc_start: 0.8991 (m-10) cc_final: 0.8706 (m-80) REVERT: C 115 ASP cc_start: 0.7575 (t70) cc_final: 0.7373 (t0) REVERT: D 611 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.7018 (p0) REVERT: D 624 ASP cc_start: 0.8705 (m-30) cc_final: 0.8471 (m-30) outliers start: 4 outliers final: 0 residues processed: 196 average time/residue: 0.3042 time to fit residues: 82.1502 Evaluate side-chains 152 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 0.0270 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 0.0770 chunk 82 optimal weight: 9.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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** B 650 GLN D 650 GLN D 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13590 Z= 0.194 Angle : 0.691 9.403 18441 Z= 0.342 Chirality : 0.048 0.261 2145 Planarity : 0.004 0.033 2325 Dihedral : 9.011 69.264 2169 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.16 % Favored : 91.46 % Rotamer: Outliers : 0.27 % Allowed : 2.85 % Favored : 96.88 % 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: -1.81 (0.21), residues: 1593 helix: 0.51 (0.27), residues: 378 sheet: -0.90 (0.25), residues: 420 loop : -2.28 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 610 HIS 0.003 0.001 HIS C 251 PHE 0.017 0.001 PHE D 573 TYR 0.030 0.001 TYR D 643 ARG 0.007 0.001 ARG D 644 *********************** 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 215 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 1.599 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: 0.8935 (mmm) cc_final: 0.8614 (mmm) REVERT: A 629 MET cc_start: 0.8613 (mmm) cc_final: 0.8007 (mmm) REVERT: A 643 TYR cc_start: 0.8906 (m-10) cc_final: 0.8689 (m-80) REVERT: B 523 LEU cc_start: 0.8588 (mm) cc_final: 0.8286 (mp) REVERT: D 530 MET cc_start: 0.8961 (mmm) cc_final: 0.8283 (mmt) REVERT: D 601 LYS cc_start: 0.8390 (pttm) cc_final: 0.8185 (pttm) REVERT: D 624 ASP cc_start: 0.8711 (m-30) cc_final: 0.8486 (m-30) outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.2990 time to fit residues: 88.6391 Evaluate side-chains 155 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 87 optimal weight: 0.0770 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.6142 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13590 Z= 0.212 Angle : 0.707 9.459 18441 Z= 0.350 Chirality : 0.048 0.271 2145 Planarity : 0.004 0.038 2325 Dihedral : 8.818 67.282 2169 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.66 % Favored : 90.96 % Rotamer: Outliers : 0.14 % Allowed : 1.56 % Favored : 98.31 % 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: 0.47 (0.26), residues: 378 sheet: -0.54 (0.26), residues: 390 loop : -2.34 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 610 HIS 0.003 0.001 HIS G 251 PHE 0.018 0.002 PHE B 573 TYR 0.031 0.001 TYR B 643 ARG 0.014 0.001 ARG A 644 *********************** 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 203 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.639 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: A 530 MET cc_start: 0.8917 (mmm) cc_final: 0.8542 (mmm) REVERT: A 629 MET cc_start: 0.8567 (mmm) cc_final: 0.8105 (mmm) REVERT: A 643 TYR cc_start: 0.8876 (m-10) cc_final: 0.8525 (m-80) REVERT: B 523 LEU cc_start: 0.8606 (mm) cc_final: 0.8379 (mp) REVERT: C 304 MET cc_start: 0.8540 (mmm) cc_final: 0.8184 (mmp) REVERT: D 530 MET cc_start: 0.8998 (mmm) cc_final: 0.8341 (mmt) REVERT: D 601 LYS cc_start: 0.8451 (pttm) cc_final: 0.8077 (pttm) REVERT: D 611 ASN cc_start: 0.7010 (OUTLIER) cc_final: 0.6706 (p0) REVERT: D 624 ASP cc_start: 0.8719 (m-30) cc_final: 0.8464 (m-30) REVERT: E 70 VAL cc_start: 0.8143 (m) cc_final: 0.7939 (p) REVERT: G 304 MET cc_start: 0.8598 (mmm) cc_final: 0.7997 (mmp) outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.2968 time to fit residues: 83.0890 Evaluate side-chains 152 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 10.0000 chunk 62 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13590 Z= 0.211 Angle : 0.705 9.362 18441 Z= 0.350 Chirality : 0.047 0.252 2145 Planarity : 0.004 0.032 2325 Dihedral : 8.562 64.631 2169 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.04 % Favored : 91.59 % Rotamer: Outliers : 0.07 % Allowed : 1.36 % Favored : 98.58 % 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: -1.63 (0.21), residues: 1593 helix: 0.57 (0.27), residues: 372 sheet: -0.69 (0.25), residues: 414 loop : -2.15 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 610 HIS 0.003 0.001 HIS G 251 PHE 0.019 0.001 PHE D 573 TYR 0.033 0.002 TYR B 643 ARG 0.011 0.001 ARG A 644 *********************** 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 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.555 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: A 530 MET cc_start: 0.8984 (mmm) cc_final: 0.8604 (mmm) REVERT: A 629 MET cc_start: 0.8630 (mmm) cc_final: 0.8191 (mmm) REVERT: A 643 TYR cc_start: 0.8905 (m-10) cc_final: 0.8643 (m-80) REVERT: D 601 LYS cc_start: 0.8473 (pttm) cc_final: 0.8144 (pttm) REVERT: D 611 ASN cc_start: 0.6955 (OUTLIER) cc_final: 0.6698 (p0) REVERT: D 624 ASP cc_start: 0.8700 (m-30) cc_final: 0.8422 (m-30) REVERT: E 70 VAL cc_start: 0.8135 (m) cc_final: 0.7925 (p) REVERT: G 115 ASP cc_start: 0.7530 (t70) cc_final: 0.7310 (t0) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.3061 time to fit residues: 84.1939 Evaluate side-chains 150 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.0570 chunk 114 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- 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 577 GLN D 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13590 Z= 0.229 Angle : 0.717 9.276 18441 Z= 0.354 Chirality : 0.048 0.269 2145 Planarity : 0.004 0.037 2325 Dihedral : 8.467 63.232 2169 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.35 % Favored : 91.21 % Rotamer: Outliers : 0.14 % Allowed : 0.75 % Favored : 99.12 % 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: -1.63 (0.20), residues: 1593 helix: 0.56 (0.27), residues: 378 sheet: -0.65 (0.25), residues: 414 loop : -2.19 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 610 HIS 0.003 0.001 HIS G 251 PHE 0.011 0.001 PHE G 212 TYR 0.008 0.001 TYR E 219 ARG 0.011 0.001 ARG A 644 *********************** 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 193 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.930 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: A 530 MET cc_start: 0.8983 (mmm) cc_final: 0.8483 (mmm) REVERT: A 629 MET cc_start: 0.8612 (mmm) cc_final: 0.8143 (mmm) REVERT: D 611 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6785 (p0) REVERT: D 624 ASP cc_start: 0.8696 (m-30) cc_final: 0.8414 (m-30) REVERT: G 115 ASP cc_start: 0.7592 (t70) cc_final: 0.7351 (t0) REVERT: G 304 MET cc_start: 0.8537 (mmm) cc_final: 0.7897 (mmp) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.3203 time to fit residues: 85.6143 Evaluate side-chains 145 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 128 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13590 Z= 0.240 Angle : 0.732 9.479 18441 Z= 0.364 Chirality : 0.048 0.260 2145 Planarity : 0.004 0.037 2325 Dihedral : 8.393 61.891 2169 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.41 % Favored : 91.15 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.46 % 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: -1.64 (0.20), residues: 1593 helix: 0.48 (0.27), residues: 375 sheet: -0.40 (0.26), residues: 384 loop : -2.26 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP G 114 HIS 0.003 0.001 HIS E 251 PHE 0.013 0.001 PHE E 178 TYR 0.024 0.001 TYR A 643 ARG 0.011 0.001 ARG B 644 ********************** 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 194 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.628 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: A 530 MET cc_start: 0.8998 (mmm) cc_final: 0.8499 (mmm) REVERT: A 629 MET cc_start: 0.8610 (mmm) cc_final: 0.8128 (mmm) REVERT: C 304 MET cc_start: 0.8490 (mmm) cc_final: 0.8041 (mmp) REVERT: D 611 ASN cc_start: 0.7026 (OUTLIER) cc_final: 0.6790 (p0) REVERT: D 629 MET cc_start: 0.8221 (mmm) cc_final: 0.7816 (mmm) REVERT: G 304 MET cc_start: 0.8488 (mmm) cc_final: 0.8006 (mmp) outliers start: 2 outliers final: 1 residues processed: 194 average time/residue: 0.3102 time to fit residues: 82.6613 Evaluate side-chains 143 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 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** 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 = 0.055327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.044420 restraints weight = 80500.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045979 restraints weight = 45441.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047087 restraints weight = 30727.210| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13590 Z= 0.177 Angle : 0.713 9.850 18441 Z= 0.353 Chirality : 0.048 0.257 2145 Planarity : 0.004 0.040 2325 Dihedral : 8.217 59.730 2169 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.16 % Favored : 91.40 % Rotamer: Outliers : 0.14 % Allowed : 0.34 % Favored : 99.53 % 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: -1.55 (0.20), residues: 1593 helix: 0.41 (0.27), residues: 375 sheet: -0.26 (0.26), residues: 384 loop : -2.17 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 610 HIS 0.003 0.001 HIS G 251 PHE 0.011 0.001 PHE G 212 TYR 0.036 0.001 TYR D 643 ARG 0.011 0.001 ARG D 644 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.79 seconds wall clock time: 52 minutes 54.86 seconds (3174.86 seconds total)