Starting phenix.real_space_refine on Thu Feb 15 20:23:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/02_2024/8f7t_28910_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/02_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_28910/02_2024/8f7t_28910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/02_2024/8f7t_28910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/02_2024/8f7t_28910_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7t_28910/02_2024/8f7t_28910_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 269": "OE1" <-> "OE2" Residue "G GLU 292": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.09, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 5.05 Conformation dependent library (CDL) restraints added in 2.3 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: 1.40 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: 5.45 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: 94.28 - 102.25: 59 102.25 - 110.22: 3148 110.22 - 118.19: 7560 118.19 - 126.15: 7375 126.15 - 134.12: 299 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 2.440 ... (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 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: 2.840 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: 10.410 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.490 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.870 ------------------------------------------------------------------------------- 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 : 1.663 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: 0.3043 time to fit residues: 153.8963 Evaluate side-chains 191 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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: 9.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.8224 ------------------------------------------------------------------------------- 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 A 653 GLN B 616 ASN C 105 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3422 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= 0.230 Angle : 0.793 9.484 18441 Z= 0.393 Chirality : 0.051 0.267 2145 Planarity : 0.005 0.049 2325 Dihedral : 16.556 117.418 2169 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.22 % Favored : 91.40 % Rotamer: Outliers : 1.02 % Allowed : 5.42 % Favored : 93.56 % 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: -2.22 (0.20), residues: 1593 helix: 0.12 (0.26), residues: 387 sheet: -1.13 (0.23), residues: 432 loop : -2.56 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 47 HIS 0.004 0.001 HIS C 218 PHE 0.022 0.002 PHE G 161 TYR 0.049 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 325 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 310 time to evaluate : 1.794 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: 0.8370 (mmm) cc_final: 0.7499 (mmm) REVERT: A 537 LEU cc_start: 0.8527 (mt) cc_final: 0.8292 (mt) REVERT: A 629 MET cc_start: 0.8594 (mmm) cc_final: 0.7424 (mmm) REVERT: B 530 MET cc_start: 0.8010 (mmt) cc_final: 0.7382 (mmm) REVERT: B 575 GLN cc_start: 0.8248 (pp30) cc_final: 0.7855 (tm-30) REVERT: D 611 ASN cc_start: 0.6978 (OUTLIER) cc_final: 0.6631 (p0) REVERT: G 41 TYR cc_start: 0.7228 (m-80) cc_final: 0.7006 (m-10) outliers start: 15 outliers final: 6 residues processed: 320 average time/residue: 0.2792 time to fit residues: 124.4082 Evaluate side-chains 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13590 Z= 0.252 Angle : 0.732 9.346 18441 Z= 0.364 Chirality : 0.048 0.254 2145 Planarity : 0.004 0.035 2325 Dihedral : 13.188 111.743 2169 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.42 % Favored : 90.21 % Rotamer: Outliers : 0.20 % Allowed : 4.47 % Favored : 95.33 % 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: -2.22 (0.20), residues: 1593 helix: 0.15 (0.26), residues: 387 sheet: -1.23 (0.22), residues: 435 loop : -2.52 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 571 HIS 0.004 0.001 HIS E 352 PHE 0.016 0.002 PHE G 55 TYR 0.015 0.001 TYR C 219 ARG 0.005 0.001 ARG B 579 *********************** 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 fitting. rotamer outliers: 3 poor density : 264 time to evaluate : 1.597 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: A 530 MET cc_start: 0.8497 (mmm) cc_final: 0.7802 (mmm) REVERT: A 629 MET cc_start: 0.8492 (mmm) cc_final: 0.8190 (mmm) REVERT: B 523 LEU cc_start: 0.8764 (mm) cc_final: 0.8475 (mp) REVERT: B 530 MET cc_start: 0.8105 (mmt) cc_final: 0.7253 (mmm) REVERT: D 530 MET cc_start: 0.8751 (mmm) cc_final: 0.7822 (mmm) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.2784 time to fit residues: 103.2638 Evaluate side-chains 168 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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: 0.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN D 616 ASN E 205 GLN G 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4539 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= 0.189 Angle : 0.700 9.542 18441 Z= 0.342 Chirality : 0.047 0.248 2145 Planarity : 0.004 0.033 2325 Dihedral : 9.969 73.306 2169 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.91 % Favored : 91.71 % Rotamer: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % 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: 0.13 (0.25), residues: 387 sheet: -0.82 (0.24), residues: 393 loop : -2.44 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 571 HIS 0.003 0.001 HIS G 74 PHE 0.019 0.002 PHE D 573 TYR 0.028 0.001 TYR D 643 ARG 0.005 0.000 ARG C 168 *********************** 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 235 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.575 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: A 530 MET cc_start: 0.8679 (mmm) cc_final: 0.8058 (mmm) REVERT: B 530 MET cc_start: 0.8046 (mmt) cc_final: 0.7530 (mmm) REVERT: D 530 MET cc_start: 0.8815 (mmm) cc_final: 0.7943 (mmt) REVERT: E 178 PHE cc_start: 0.8038 (m-80) cc_final: 0.7733 (m-10) REVERT: G 41 TYR cc_start: 0.7717 (m-80) cc_final: 0.7332 (m-10) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.2878 time to fit residues: 94.4686 Evaluate side-chains 170 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 64 optimal weight: 0.0980 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 140 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN G 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4849 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= 0.188 Angle : 0.685 9.519 18441 Z= 0.341 Chirality : 0.047 0.249 2145 Planarity : 0.004 0.051 2325 Dihedral : 9.257 69.415 2169 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.53 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -1.83 (0.20), residues: 1593 helix: 0.28 (0.26), residues: 390 sheet: -0.56 (0.25), residues: 390 loop : -2.39 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 596 HIS 0.002 0.001 HIS E 251 PHE 0.014 0.001 PHE E 212 TYR 0.020 0.001 TYR A 643 ARG 0.012 0.001 ARG A 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 219 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.636 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 523 LEU cc_start: 0.8561 (mm) cc_final: 0.8318 (mp) REVERT: A 530 MET cc_start: 0.8772 (mmm) cc_final: 0.8181 (mmm) REVERT: A 583 ILE cc_start: 0.9077 (pt) cc_final: 0.8862 (tt) REVERT: B 523 LEU cc_start: 0.8722 (mm) cc_final: 0.8478 (mp) REVERT: B 530 MET cc_start: 0.8220 (mmt) cc_final: 0.7616 (mmm) REVERT: C 70 VAL cc_start: 0.7912 (m) cc_final: 0.7674 (p) REVERT: C 106 MET cc_start: 0.7871 (tmm) cc_final: 0.7643 (tmm) REVERT: D 530 MET cc_start: 0.8925 (mmm) cc_final: 0.8014 (mmm) REVERT: D 624 ASP cc_start: 0.8620 (m-30) cc_final: 0.8367 (m-30) REVERT: E 178 PHE cc_start: 0.8026 (m-80) cc_final: 0.7759 (m-10) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2977 time to fit residues: 91.1214 Evaluate side-chains 158 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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: 4.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN C 205 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN E 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13590 Z= 0.183 Angle : 0.677 9.575 18441 Z= 0.335 Chirality : 0.047 0.251 2145 Planarity : 0.004 0.039 2325 Dihedral : 8.853 66.157 2169 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.53 % Favored : 92.09 % Rotamer: Outliers : 0.27 % Allowed : 2.44 % Favored : 97.29 % 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: -1.75 (0.20), residues: 1593 helix: 0.32 (0.26), residues: 396 sheet: -0.58 (0.25), residues: 390 loop : -2.29 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 610 HIS 0.002 0.001 HIS E 251 PHE 0.010 0.001 PHE C 376 TYR 0.028 0.001 TYR D 643 ARG 0.010 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 : 1.688 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 523 LEU cc_start: 0.8572 (mm) cc_final: 0.8348 (mp) REVERT: A 530 MET cc_start: 0.8810 (mmm) cc_final: 0.8264 (mmm) REVERT: B 523 LEU cc_start: 0.8603 (mm) cc_final: 0.8332 (mp) REVERT: B 530 MET cc_start: 0.8272 (mmt) cc_final: 0.7841 (mmm) REVERT: C 70 VAL cc_start: 0.7866 (m) cc_final: 0.7665 (p) REVERT: D 624 ASP cc_start: 0.8590 (m-30) cc_final: 0.8326 (m-30) REVERT: D 643 TYR cc_start: 0.8627 (m-80) cc_final: 0.8370 (m-80) REVERT: E 102 MET cc_start: 0.7737 (mtp) cc_final: 0.7461 (mtt) REVERT: E 178 PHE cc_start: 0.8025 (m-80) cc_final: 0.7540 (m-10) REVERT: G 304 MET cc_start: 0.8408 (mmm) cc_final: 0.8141 (mmp) outliers start: 4 outliers final: 1 residues processed: 214 average time/residue: 0.3001 time to fit residues: 89.3734 Evaluate side-chains 156 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 97 optimal weight: 0.0670 chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN C 205 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN E 205 GLN G 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13590 Z= 0.180 Angle : 0.681 9.462 18441 Z= 0.338 Chirality : 0.047 0.259 2145 Planarity : 0.004 0.042 2325 Dihedral : 8.523 62.692 2169 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.78 % Favored : 91.84 % Rotamer: Outliers : 0.14 % Allowed : 2.24 % 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: -1.67 (0.20), residues: 1593 helix: -0.02 (0.26), residues: 414 sheet: -0.45 (0.25), residues: 390 loop : -2.10 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 610 HIS 0.002 0.000 HIS C 251 PHE 0.016 0.001 PHE D 573 TYR 0.024 0.001 TYR D 643 ARG 0.017 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 218 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.617 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: 0.8800 (mmm) cc_final: 0.8242 (mmm) REVERT: A 629 MET cc_start: 0.7959 (mmm) cc_final: 0.7496 (mmm) REVERT: B 523 LEU cc_start: 0.8586 (mm) cc_final: 0.8343 (mp) REVERT: B 530 MET cc_start: 0.8341 (mmt) cc_final: 0.7904 (mmm) REVERT: B 575 GLN cc_start: 0.8198 (pp30) cc_final: 0.7961 (tm-30) REVERT: B 639 THR cc_start: 0.9067 (m) cc_final: 0.8456 (p) REVERT: C 304 MET cc_start: 0.8374 (mmm) cc_final: 0.8169 (mmp) REVERT: D 624 ASP cc_start: 0.8588 (m-30) cc_final: 0.8308 (m-30) REVERT: D 629 MET cc_start: 0.8338 (mmm) cc_final: 0.8019 (mmm) REVERT: E 102 MET cc_start: 0.7899 (mtp) cc_final: 0.7664 (mtt) REVERT: E 178 PHE cc_start: 0.7977 (m-80) cc_final: 0.7589 (m-10) REVERT: G 304 MET cc_start: 0.8369 (mmm) cc_final: 0.8012 (mmp) outliers start: 2 outliers final: 1 residues processed: 218 average time/residue: 0.2998 time to fit residues: 90.2142 Evaluate side-chains 156 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13590 Z= 0.221 Angle : 0.692 9.455 18441 Z= 0.345 Chirality : 0.047 0.346 2145 Planarity : 0.004 0.053 2325 Dihedral : 8.463 60.399 2169 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.53 % Favored : 92.09 % Rotamer: Outliers : 0.07 % Allowed : 1.63 % 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: -1.56 (0.21), residues: 1593 helix: 0.38 (0.27), residues: 387 sheet: -0.38 (0.25), residues: 390 loop : -2.13 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 610 HIS 0.003 0.001 HIS G 251 PHE 0.010 0.001 PHE C 376 TYR 0.026 0.001 TYR A 643 ARG 0.012 0.001 ARG D 633 *********************** 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 207 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 1.595 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 523 LEU cc_start: 0.8635 (mm) cc_final: 0.8268 (mp) REVERT: A 530 MET cc_start: 0.8841 (mmm) cc_final: 0.8467 (mmm) REVERT: B 523 LEU cc_start: 0.8656 (mm) cc_final: 0.8401 (mp) REVERT: B 530 MET cc_start: 0.8461 (mmt) cc_final: 0.8049 (mmm) REVERT: B 639 THR cc_start: 0.8942 (m) cc_final: 0.8727 (p) REVERT: D 530 MET cc_start: 0.9003 (mmm) cc_final: 0.8220 (mmt) REVERT: D 624 ASP cc_start: 0.8578 (m-30) cc_final: 0.8342 (m-30) REVERT: D 629 MET cc_start: 0.8377 (mmm) cc_final: 0.8131 (mmm) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.3203 time to fit residues: 92.2067 Evaluate side-chains 145 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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: 2.9990 chunk 136 optimal weight: 0.0470 chunk 145 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.0980 chunk 131 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13590 Z= 0.210 Angle : 0.703 9.431 18441 Z= 0.353 Chirality : 0.047 0.267 2145 Planarity : 0.004 0.045 2325 Dihedral : 8.309 58.145 2169 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.78 % Favored : 91.84 % Rotamer: Outliers : 0.07 % Allowed : 1.15 % Favored : 98.78 % 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: -1.61 (0.20), residues: 1593 helix: 0.10 (0.26), residues: 396 sheet: -0.19 (0.27), residues: 351 loop : -2.11 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 571 HIS 0.003 0.001 HIS G 251 PHE 0.012 0.001 PHE E 178 TYR 0.048 0.001 TYR B 643 ARG 0.010 0.001 ARG B 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 204 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.732 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 523 LEU cc_start: 0.8688 (mm) cc_final: 0.8308 (mp) REVERT: A 530 MET cc_start: 0.8864 (mmm) cc_final: 0.8551 (mmm) REVERT: B 523 LEU cc_start: 0.8831 (mm) cc_final: 0.8483 (mp) REVERT: B 530 MET cc_start: 0.8526 (mmt) cc_final: 0.8095 (mmm) REVERT: B 575 GLN cc_start: 0.8261 (pp30) cc_final: 0.7120 (pp30) REVERT: D 530 MET cc_start: 0.9014 (mmm) cc_final: 0.8544 (mmm) REVERT: D 624 ASP cc_start: 0.8561 (m-30) cc_final: 0.8305 (m-30) REVERT: D 629 MET cc_start: 0.8481 (mmm) cc_final: 0.8242 (mmm) REVERT: E 70 VAL cc_start: 0.7872 (m) cc_final: 0.7625 (p) REVERT: G 304 MET cc_start: 0.8504 (mmm) cc_final: 0.8039 (mmp) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.3090 time to fit residues: 87.4071 Evaluate side-chains 143 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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: 0.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.0000 chunk 102 optimal weight: 10.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13590 Z= 0.189 Angle : 0.739 10.549 18441 Z= 0.368 Chirality : 0.048 0.251 2145 Planarity : 0.004 0.058 2325 Dihedral : 8.202 57.950 2169 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.28 % Favored : 92.34 % Rotamer: Outliers : 0.07 % Allowed : 0.88 % Favored : 99.05 % 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: -1.57 (0.20), residues: 1593 helix: 0.06 (0.27), residues: 396 sheet: -0.17 (0.27), residues: 351 loop : -2.05 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 571 HIS 0.002 0.000 HIS G 251 PHE 0.011 0.001 PHE D 573 TYR 0.013 0.001 TYR B 638 ARG 0.013 0.001 ARG A 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 205 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 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: A 523 LEU cc_start: 0.8554 (mm) cc_final: 0.8165 (mp) REVERT: A 530 MET cc_start: 0.8828 (mmm) cc_final: 0.8353 (mmt) REVERT: A 629 MET cc_start: 0.8009 (mmm) cc_final: 0.7576 (mmm) REVERT: B 530 MET cc_start: 0.8542 (mmt) cc_final: 0.8143 (mmm) REVERT: C 304 MET cc_start: 0.8343 (mmm) cc_final: 0.8084 (mmp) REVERT: D 530 MET cc_start: 0.8989 (mmm) cc_final: 0.8289 (mmt) REVERT: D 624 ASP cc_start: 0.8485 (m-30) cc_final: 0.8230 (m-30) REVERT: D 629 MET cc_start: 0.8490 (mmm) cc_final: 0.8266 (mmm) REVERT: G 304 MET cc_start: 0.8492 (mmm) cc_final: 0.8127 (mmp) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.3037 time to fit residues: 86.0938 Evaluate side-chains 144 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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: 0.0270 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.056099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045093 restraints weight = 80750.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046654 restraints weight = 45959.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047787 restraints weight = 31054.291| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13590 Z= 0.216 Angle : 0.713 9.423 18441 Z= 0.357 Chirality : 0.047 0.251 2145 Planarity : 0.004 0.050 2325 Dihedral : 8.062 57.939 2169 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.10 % Favored : 91.53 % Rotamer: Outliers : 0.07 % Allowed : 0.68 % Favored : 99.25 % 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: -1.53 (0.20), residues: 1593 helix: -0.00 (0.26), residues: 396 sheet: -0.11 (0.27), residues: 345 loop : -1.97 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 571 HIS 0.004 0.001 HIS E 330 PHE 0.011 0.001 PHE G 212 TYR 0.036 0.001 TYR D 643 ARG 0.013 0.001 ARG B 633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2828.33 seconds wall clock time: 52 minutes 27.35 seconds (3147.35 seconds total)