Starting phenix.real_space_refine on Sun Mar 17 15:23:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/03_2024/7mo7_23919_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/03_2024/7mo7_23919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/03_2024/7mo7_23919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/03_2024/7mo7_23919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/03_2024/7mo7_23919_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/03_2024/7mo7_23919_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 161 5.16 5 C 11430 2.51 5 N 3128 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18135 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2287 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Chain: "E" Number of atoms: 5324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5324 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 654} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 4937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4937 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 595} Chain breaks: 6 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 154 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 5490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5490 Classifications: {'peptide': 699} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {'IDS': 3, 'SGN': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 9.52, per 1000 atoms: 0.52 Number of scatterers: 18135 At special positions: 0 Unit cell: (154.44, 181.44, 168.48, 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 161 16.00 O 3416 8.00 N 3128 7.00 C 11430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 469 " distance=2.03 Simple disulfide: pdb=" SG CYS D 412 " - pdb=" SG CYS D 452 " distance=2.03 Simple disulfide: pdb=" SG CYS D 440 " - pdb=" SG CYS D 464 " distance=2.03 Simple disulfide: pdb=" SG CYS D 519 " - pdb=" SG CYS D 535 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 679 " distance=2.04 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 658 " distance=2.03 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 584 " distance=2.03 Simple disulfide: pdb=" SG CYS E 95 " - pdb=" SG CYS E 101 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 409 " distance=2.04 Simple disulfide: pdb=" SG CYS E 298 " - pdb=" SG CYS E 363 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 397 " distance=2.03 Simple disulfide: pdb=" SG CYS E 520 " - pdb=" SG CYS E 538 " distance=2.03 Simple disulfide: pdb=" SG CYS E 526 " - pdb=" SG CYS E 561 " distance=2.02 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 545 " distance=2.03 Simple disulfide: pdb=" SG CYS E 541 " - pdb=" SG CYS E 551 " distance=2.03 Simple disulfide: pdb=" SG CYS E 610 " - pdb=" SG CYS E 624 " distance=2.03 Simple disulfide: pdb=" SG CYS E 697 " - pdb=" SG CYS E 709 " distance=2.04 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 377 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 452 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 519 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 679 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 397 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 709 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " IDS F 2 " - " SGN F 3 " " IDS F 4 " - " SGN F 5 " BETA1-4 " SGN F 1 " - " IDS F 2 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN F 3 " - " IDS F 4 " " SGN F 5 " - " IDS F 6 " Time building additional restraints: 7.06 Conformation dependent library (CDL) restraints added in 3.4 seconds 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 39 sheets defined 8.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 415 through 425 Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 639 through 646 Processing helix chain 'D' and resid 709 through 720 removed outlier: 4.168A pdb=" N LYS D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP D 715 " --> pdb=" O TYR D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 203 through 208 Proline residue: E 207 - end of helix No H-bonds generated for 'chain 'E' and resid 203 through 208' Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 327 through 332 removed outlier: 3.765A pdb=" N ARG E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 327 through 332' Processing helix chain 'E' and resid 367 through 375 Processing helix chain 'E' and resid 387 through 390 No H-bonds generated for 'chain 'E' and resid 387 through 390' Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 526 through 531 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 639 through 645 Processing helix chain 'A' and resid 709 through 711 No H-bonds generated for 'chain 'A' and resid 709 through 711' Processing helix chain 'A' and resid 713 through 721 removed outlier: 4.115A pdb=" N LEU A 721 " --> pdb=" O HIS A 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 367 through 375 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing sheet with id= A, first strand: chain 'D' and resid 451 through 453 Processing sheet with id= B, first strand: chain 'D' and resid 563 through 565 removed outlier: 4.186A pdb=" N CYS D 519 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR D 513 " --> pdb=" O HIS D 517 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N HIS D 517 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLY D 520 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA D 532 " --> pdb=" O GLY D 520 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 611 through 616 Processing sheet with id= D, first strand: chain 'D' and resid 656 through 659 removed outlier: 6.652A pdb=" N LEU D 677 " --> pdb=" O LEU D 688 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'E' and resid 52 through 58 removed outlier: 6.726A pdb=" N GLY E 65 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL E 55 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE E 63 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU E 57 " --> pdb=" O HIS E 61 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 82 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 89 through 91 Processing sheet with id= H, first strand: chain 'E' and resid 119 through 123 removed outlier: 4.033A pdb=" N ALA E 119 " --> pdb=" O CYS E 133 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS E 141 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 182 through 188 Processing sheet with id= J, first strand: chain 'E' and resid 424 through 427 removed outlier: 4.256A pdb=" N THR E 276 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N CYS E 298 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 13.541A pdb=" N PHE E 274 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 281 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL E 264 " --> pdb=" O TYR E 249 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR E 249 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 298 through 300 removed outlier: 4.001A pdb=" N CYS E 298 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 477 through 480 removed outlier: 3.609A pdb=" N VAL E 477 " --> pdb=" O GLN E 464 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 441 " --> pdb=" O GLY E 456 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 538 through 540 Processing sheet with id= N, first strand: chain 'E' and resid 621 through 625 removed outlier: 6.561A pdb=" N TRP E 586 " --> pdb=" O ILE E 565 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE E 565 " --> pdb=" O TRP E 586 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 601 through 605 Processing sheet with id= P, first strand: chain 'E' and resid 658 through 663 removed outlier: 6.905A pdb=" N THR E 678 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE E 662 " --> pdb=" O THR E 676 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR E 676 " --> pdb=" O ILE E 662 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR E 710 " --> pdb=" O LEU E 699 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU E 699 " --> pdb=" O TYR E 710 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 316 through 324 removed outlier: 6.771A pdb=" N VAL E 345 " --> pdb=" O GLN E 318 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA E 320 " --> pdb=" O PHE E 343 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE E 343 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 322 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 341 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG E 359 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 49 through 52 Processing sheet with id= S, first strand: chain 'A' and resid 61 through 63 removed outlier: 3.519A pdb=" N GLN A 95 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 90 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 188 through 190 Processing sheet with id= U, first strand: chain 'A' and resid 270 through 272 Processing sheet with id= V, first strand: chain 'A' and resid 451 through 453 Processing sheet with id= W, first strand: chain 'A' and resid 563 through 565 removed outlier: 8.112A pdb=" N GLY A 520 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA A 532 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 612 through 616 Processing sheet with id= Y, first strand: chain 'A' and resid 656 through 659 Processing sheet with id= Z, first strand: chain 'A' and resid 676 through 680 removed outlier: 5.865A pdb=" N CYS A 679 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 687 " --> pdb=" O CYS A 679 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 44 through 47 Processing sheet with id= AB, first strand: chain 'B' and resid 52 through 58 removed outlier: 7.052A pdb=" N GLY B 65 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL B 55 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 63 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 57 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 82 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN B 74 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 80 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 121 through 123 Processing sheet with id= AD, first strand: chain 'B' and resid 181 through 189 Processing sheet with id= AE, first strand: chain 'B' and resid 424 through 427 removed outlier: 4.511A pdb=" N THR B 276 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 281 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 259 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 264 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR B 249 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 298 through 300 removed outlier: 4.018A pdb=" N CYS B 298 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 360 through 366 removed outlier: 3.754A pdb=" N ALA B 319 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B 347 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 317 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 383 through 385 Processing sheet with id= AI, first strand: chain 'B' and resid 463 through 467 removed outlier: 4.775A pdb=" N THR B 451 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 621 through 624 removed outlier: 6.376A pdb=" N TRP B 586 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE B 565 " --> pdb=" O TRP B 586 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 602 through 604 Processing sheet with id= AL, first strand: chain 'B' and resid 674 through 678 removed outlier: 3.507A pdb=" N CYS B 709 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR B 710 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU B 699 " --> pdb=" O TYR B 710 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 689 through 691 397 hydrogen bonds defined for protein. 1053 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: 8.29 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5913 1.34 - 1.46: 4347 1.46 - 1.58: 8116 1.58 - 1.71: 3 1.71 - 1.83: 195 Bond restraints: 18574 Sorted by residual: bond pdb=" O6 SGN F 1 " pdb=" S2 SGN F 1 " ideal model delta sigma weight residual 1.660 1.526 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" O6 SGN F 3 " pdb=" S2 SGN F 3 " ideal model delta sigma weight residual 1.660 1.527 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O2 IDS F 6 " pdb=" S IDS F 6 " ideal model delta sigma weight residual 1.646 1.529 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" N SGN F 3 " pdb=" S1 SGN F 3 " ideal model delta sigma weight residual 1.713 1.602 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" O2 IDS F 2 " pdb=" S IDS F 2 " ideal model delta sigma weight residual 1.646 1.536 0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 18569 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.21: 396 105.21 - 112.43: 9471 112.43 - 119.64: 6007 119.64 - 126.85: 9083 126.85 - 134.07: 291 Bond angle restraints: 25248 Sorted by residual: angle pdb=" C2 SGN F 1 " pdb=" N SGN F 1 " pdb=" S1 SGN F 1 " ideal model delta sigma weight residual 119.97 106.49 13.48 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C LEU D 523 " pdb=" N ILE D 524 " pdb=" CA ILE D 524 " ideal model delta sigma weight residual 123.08 119.49 3.59 1.01e+00 9.80e-01 1.26e+01 angle pdb=" C2 SGN F 3 " pdb=" N SGN F 3 " pdb=" S1 SGN F 3 " ideal model delta sigma weight residual 119.97 109.35 10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1S IDS F 2 " pdb=" S IDS F 2 " pdb=" O2 IDS F 2 " ideal model delta sigma weight residual 101.14 111.59 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C ILE B 726 " pdb=" N ASP B 727 " pdb=" CA ASP B 727 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.10e+01 ... (remaining 25243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 10528 25.33 - 50.67: 597 50.67 - 76.00: 73 76.00 - 101.34: 29 101.34 - 126.67: 23 Dihedral angle restraints: 11250 sinusoidal: 4518 harmonic: 6732 Sorted by residual: dihedral pdb=" CB CYS A 177 " pdb=" SG CYS A 177 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual 93.00 -177.31 -89.69 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS D 412 " pdb=" SG CYS D 412 " pdb=" SG CYS D 452 " pdb=" CB CYS D 452 " ideal model delta sinusoidal sigma weight residual 93.00 179.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 305 " pdb=" SG CYS A 305 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -165.50 79.50 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 11247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2155 0.050 - 0.099: 498 0.099 - 0.149: 142 0.149 - 0.198: 6 0.198 - 0.248: 3 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C1 SGN F 3 " pdb=" O4 IDS F 2 " pdb=" C2 SGN F 3 " pdb=" O5 SGN F 3 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 1.90e+01 chirality pdb=" C1 IDS F 2 " pdb=" O4 SGN F 1 " pdb=" C2 IDS F 2 " pdb=" O5 IDS F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.79e+01 chirality pdb=" C1 IDS F 4 " pdb=" O4 SGN F 3 " pdb=" C2 IDS F 4 " pdb=" O5 IDS F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.31e+00 ... (remaining 2801 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 442 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 443 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 443 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 443 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 459 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 460 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 569 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO E 570 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 570 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 570 " 0.023 5.00e-02 4.00e+02 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 555 2.68 - 3.24: 18390 3.24 - 3.79: 29109 3.79 - 4.35: 38952 4.35 - 4.90: 61101 Nonbonded interactions: 148107 Sorted by model distance: nonbonded pdb=" O THR E 230 " pdb=" OG SER E 233 " model vdw 2.126 2.440 nonbonded pdb=" O SER B 684 " pdb=" NH2 ARG B 688 " model vdw 2.150 2.520 nonbonded pdb=" OG1 THR D 454 " pdb=" O ILE D 459 " model vdw 2.154 2.440 nonbonded pdb=" N TYR E 566 " pdb=" O CYS E 584 " model vdw 2.164 2.520 nonbonded pdb=" OG1 THR A 38 " pdb=" OG1 THR A 75 " model vdw 2.166 2.440 ... (remaining 148102 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 'B' and (resid 26 through 106 or resid 111 through 301 or resid 311 throu \ gh 664 or (resid 665 through 666 and (name N or name CA or name C or name O or n \ ame CB )) or resid 667 through 668 or (resid 669 through 670 and (name N or name \ CA or name C or name O or name CB )) or resid 671 through 680 or (resid 687 thr \ ough 689 and (name N or name CA or name C or name O or name CB )) or resid 690 t \ hrough 694 or (resid 695 and (name N or name CA or name C or name O or name CB ) \ ) or resid 696 through 699 or (resid 700 and (name N or name CA or name C or nam \ e O or name CB )) or resid 701 through 707 or (resid 708 and (name N or name CA \ or name C or name O or name CB )) or resid 709 or (resid 710 and (name N or name \ CA or name C or name O or name CB )) or resid 711 through 718 or (resid 719 and \ (name N or name CA or name C or name O or name CB )) or resid 720 through 722 o \ r (resid 723 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 24 or (resid 725 and (name N or name CA or name C or name O or name CB )) or res \ id 726 through 730 or (resid 731 through 732 and (name N or name CA or name C or \ name O or name CB )) or resid 733 through 738)) selection = (chain 'E' and (resid 26 through 106 or resid 111 through 738)) } 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: 1.640 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: 5.320 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 52.020 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 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:3.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.004 0.134 18574 Z= 0.303 Angle : 0.745 13.482 25248 Z= 0.394 Chirality : 0.046 0.248 2804 Planarity : 0.004 0.056 3256 Dihedral : 16.294 126.669 6759 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.19 (0.17), residues: 2291 helix: -0.57 (0.44), residues: 148 sheet: -0.19 (0.22), residues: 517 loop : -1.06 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 617 HIS 0.011 0.001 HIS B 275 PHE 0.021 0.002 PHE E 192 TYR 0.014 0.001 TYR B 291 ARG 0.004 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 130 LEU cc_start: 0.9596 (tp) cc_final: 0.9304 (tt) REVERT: E 357 MET cc_start: 0.8873 (mtm) cc_final: 0.8523 (mtm) REVERT: A 615 TYR cc_start: 0.6943 (m-10) cc_final: 0.6581 (m-10) REVERT: A 688 LEU cc_start: 0.7955 (mm) cc_final: 0.7628 (mm) REVERT: B 288 LEU cc_start: 0.8004 (mp) cc_final: 0.7497 (mp) REVERT: B 340 ASP cc_start: 0.6580 (m-30) cc_final: 0.6264 (m-30) REVERT: B 357 MET cc_start: 0.7727 (mpp) cc_final: 0.7485 (mpp) REVERT: B 434 PHE cc_start: 0.8456 (m-80) cc_final: 0.8214 (m-80) REVERT: B 463 MET cc_start: 0.8562 (ptp) cc_final: 0.7980 (mpp) REVERT: B 581 LEU cc_start: 0.8735 (mt) cc_final: 0.8326 (tp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3065 time to fit residues: 54.6393 Evaluate side-chains 76 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 448 HIS D 682 HIS ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 18574 Z= 0.393 Angle : 0.764 9.467 25248 Z= 0.398 Chirality : 0.048 0.257 2804 Planarity : 0.006 0.051 3256 Dihedral : 12.146 103.327 2629 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.10 % Allowed : 9.55 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2291 helix: -1.32 (0.40), residues: 150 sheet: -0.51 (0.22), residues: 514 loop : -1.17 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 428 HIS 0.021 0.002 HIS B 494 PHE 0.031 0.003 PHE E 398 TYR 0.026 0.002 TYR B 416 ARG 0.026 0.001 ARG D 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 130 LEU cc_start: 0.9697 (tp) cc_final: 0.9256 (tt) REVERT: E 357 MET cc_start: 0.8886 (mtm) cc_final: 0.8487 (mtm) REVERT: E 431 MET cc_start: 0.8016 (pmm) cc_final: 0.7745 (pmm) REVERT: E 455 LEU cc_start: 0.9163 (mp) cc_final: 0.8880 (mp) REVERT: B 288 LEU cc_start: 0.8129 (mp) cc_final: 0.7678 (mp) REVERT: B 340 ASP cc_start: 0.6823 (m-30) cc_final: 0.6484 (m-30) REVERT: B 357 MET cc_start: 0.8060 (mpp) cc_final: 0.7529 (mpp) REVERT: B 463 MET cc_start: 0.8708 (ptp) cc_final: 0.7771 (mpp) REVERT: B 581 LEU cc_start: 0.8509 (mt) cc_final: 0.8298 (mt) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.2621 time to fit residues: 35.7672 Evaluate side-chains 64 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 0.0170 chunk 142 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 226 optimal weight: 50.0000 chunk 186 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 167 optimal weight: 30.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS E 199 ASN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 ASN E 494 HIS ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18574 Z= 0.213 Angle : 0.631 8.895 25248 Z= 0.322 Chirality : 0.047 0.235 2804 Planarity : 0.004 0.059 3256 Dihedral : 11.017 94.632 2629 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.29 (0.17), residues: 2291 helix: -0.76 (0.43), residues: 150 sheet: -0.37 (0.22), residues: 524 loop : -1.07 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 428 HIS 0.009 0.001 HIS B 275 PHE 0.026 0.002 PHE B 374 TYR 0.016 0.002 TYR B 416 ARG 0.009 0.001 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 582 MET cc_start: 0.5099 (ppp) cc_final: 0.4779 (ppp) REVERT: E 130 LEU cc_start: 0.9689 (tp) cc_final: 0.9332 (tt) REVERT: E 195 PHE cc_start: 0.9328 (m-10) cc_final: 0.9049 (m-80) REVERT: E 357 MET cc_start: 0.8845 (mtm) cc_final: 0.8498 (mtm) REVERT: E 455 LEU cc_start: 0.9325 (mp) cc_final: 0.8844 (mp) REVERT: B 288 LEU cc_start: 0.8092 (mp) cc_final: 0.7626 (mp) REVERT: B 340 ASP cc_start: 0.6626 (m-30) cc_final: 0.6319 (m-30) REVERT: B 357 MET cc_start: 0.8139 (mpp) cc_final: 0.7751 (mpp) REVERT: B 463 MET cc_start: 0.8647 (ptp) cc_final: 0.7734 (mpp) REVERT: B 581 LEU cc_start: 0.8370 (mt) cc_final: 0.7939 (tp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2932 time to fit residues: 40.4065 Evaluate side-chains 66 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 40.0000 chunk 99 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 681 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 ASN ** E 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 ASN A 322 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18574 Z= 0.294 Angle : 0.672 8.919 25248 Z= 0.345 Chirality : 0.047 0.248 2804 Planarity : 0.005 0.056 3256 Dihedral : 10.245 90.391 2629 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 28.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.38 (0.17), residues: 2291 helix: -0.97 (0.42), residues: 148 sheet: -0.50 (0.22), residues: 536 loop : -1.10 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 617 HIS 0.017 0.002 HIS B 275 PHE 0.022 0.002 PHE B 162 TYR 0.016 0.002 TYR B 416 ARG 0.014 0.001 ARG D 533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 582 MET cc_start: 0.5523 (ppp) cc_final: 0.5130 (ppp) REVERT: E 130 LEU cc_start: 0.9722 (tp) cc_final: 0.9370 (tt) REVERT: E 195 PHE cc_start: 0.9345 (m-10) cc_final: 0.9046 (m-80) REVERT: E 357 MET cc_start: 0.8875 (mtm) cc_final: 0.8404 (mtm) REVERT: E 431 MET cc_start: 0.8122 (pmm) cc_final: 0.7581 (pmm) REVERT: E 455 LEU cc_start: 0.9277 (mp) cc_final: 0.8706 (mp) REVERT: B 288 LEU cc_start: 0.8149 (mp) cc_final: 0.7643 (mp) REVERT: B 340 ASP cc_start: 0.6591 (m-30) cc_final: 0.6346 (m-30) REVERT: B 357 MET cc_start: 0.8225 (mpp) cc_final: 0.7942 (mpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2632 time to fit residues: 35.0500 Evaluate side-chains 63 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 165 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 113 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 418 ASN D 534 GLN D 681 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18574 Z= 0.310 Angle : 0.686 11.090 25248 Z= 0.353 Chirality : 0.048 0.304 2804 Planarity : 0.005 0.071 3256 Dihedral : 9.547 89.346 2629 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.44 (0.17), residues: 2291 helix: -1.07 (0.42), residues: 148 sheet: -0.56 (0.22), residues: 523 loop : -1.13 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 617 HIS 0.019 0.002 HIS B 275 PHE 0.025 0.002 PHE B 162 TYR 0.020 0.002 TYR B 416 ARG 0.015 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 582 MET cc_start: 0.6175 (ppp) cc_final: 0.5894 (ppp) REVERT: E 130 LEU cc_start: 0.9635 (tp) cc_final: 0.9393 (tp) REVERT: E 226 PHE cc_start: 0.8440 (m-80) cc_final: 0.7941 (m-80) REVERT: E 357 MET cc_start: 0.8914 (mtm) cc_final: 0.8396 (mtm) REVERT: E 455 LEU cc_start: 0.9281 (mp) cc_final: 0.8710 (mp) REVERT: A 339 MET cc_start: 0.7935 (ppp) cc_final: 0.7610 (ppp) REVERT: B 288 LEU cc_start: 0.8181 (mp) cc_final: 0.7631 (mp) REVERT: B 340 ASP cc_start: 0.6528 (m-30) cc_final: 0.6328 (m-30) REVERT: B 357 MET cc_start: 0.8200 (mpp) cc_final: 0.7991 (mpp) REVERT: B 636 MET cc_start: 0.8694 (tpt) cc_final: 0.8475 (tpp) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.2490 time to fit residues: 33.0638 Evaluate side-chains 66 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 10.0000 chunk 200 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 0.0020 chunk 116 optimal weight: 0.8980 overall best weight: 1.9628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** E 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 645 HIS ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18574 Z= 0.175 Angle : 0.615 9.141 25248 Z= 0.310 Chirality : 0.047 0.345 2804 Planarity : 0.004 0.059 3256 Dihedral : 8.942 92.262 2629 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.32 (0.17), residues: 2291 helix: -1.04 (0.40), residues: 158 sheet: -0.38 (0.22), residues: 525 loop : -1.06 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 428 HIS 0.012 0.001 HIS A 645 PHE 0.015 0.001 PHE A 190 TYR 0.019 0.001 TYR D 602 ARG 0.010 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 582 MET cc_start: 0.6158 (ppp) cc_final: 0.5820 (ppp) REVERT: E 130 LEU cc_start: 0.9607 (tp) cc_final: 0.9370 (tp) REVERT: E 226 PHE cc_start: 0.8461 (m-80) cc_final: 0.8118 (m-80) REVERT: E 357 MET cc_start: 0.8843 (mtm) cc_final: 0.8356 (mtm) REVERT: E 431 MET cc_start: 0.8274 (pmm) cc_final: 0.8048 (pmm) REVERT: E 455 LEU cc_start: 0.9291 (mp) cc_final: 0.8703 (mp) REVERT: A 339 MET cc_start: 0.8072 (ppp) cc_final: 0.7806 (ppp) REVERT: B 288 LEU cc_start: 0.8066 (mp) cc_final: 0.7466 (mp) REVERT: B 340 ASP cc_start: 0.6670 (m-30) cc_final: 0.6449 (m-30) REVERT: B 357 MET cc_start: 0.7936 (mpp) cc_final: 0.7554 (mpp) REVERT: B 434 PHE cc_start: 0.8528 (m-80) cc_final: 0.8263 (m-80) REVERT: B 463 MET cc_start: 0.8709 (ptp) cc_final: 0.7369 (mpp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2741 time to fit residues: 39.6243 Evaluate side-chains 68 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 162 optimal weight: 0.0020 chunk 125 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 221 optimal weight: 40.0000 chunk 138 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18574 Z= 0.244 Angle : 0.626 9.208 25248 Z= 0.321 Chirality : 0.046 0.347 2804 Planarity : 0.005 0.050 3256 Dihedral : 8.804 91.763 2629 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.33 (0.17), residues: 2291 helix: -1.11 (0.41), residues: 154 sheet: -0.38 (0.22), residues: 533 loop : -1.08 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 428 HIS 0.012 0.001 HIS B 275 PHE 0.018 0.002 PHE B 162 TYR 0.014 0.002 TYR A 572 ARG 0.006 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 582 MET cc_start: 0.6250 (ppp) cc_final: 0.5793 (ppp) REVERT: E 130 LEU cc_start: 0.9653 (tp) cc_final: 0.9419 (tp) REVERT: E 226 PHE cc_start: 0.8468 (m-80) cc_final: 0.8143 (m-80) REVERT: E 357 MET cc_start: 0.8883 (mtm) cc_final: 0.8352 (mtm) REVERT: E 374 PHE cc_start: 0.8931 (m-10) cc_final: 0.8698 (m-80) REVERT: E 431 MET cc_start: 0.8220 (pmm) cc_final: 0.7933 (pmm) REVERT: E 455 LEU cc_start: 0.9295 (mp) cc_final: 0.8712 (mp) REVERT: A 508 MET cc_start: 0.7974 (mpp) cc_final: 0.7695 (mpp) REVERT: B 288 LEU cc_start: 0.8219 (mp) cc_final: 0.7630 (mp) REVERT: B 357 MET cc_start: 0.7982 (mpp) cc_final: 0.7635 (mpp) REVERT: B 463 MET cc_start: 0.8719 (ptp) cc_final: 0.7425 (mpp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2527 time to fit residues: 34.5671 Evaluate side-chains 62 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 chunk 174 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18574 Z= 0.282 Angle : 0.666 9.148 25248 Z= 0.344 Chirality : 0.047 0.355 2804 Planarity : 0.005 0.049 3256 Dihedral : 8.614 85.639 2629 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 27.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.41 (0.18), residues: 2291 helix: -1.03 (0.43), residues: 146 sheet: -0.56 (0.22), residues: 535 loop : -1.10 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 428 HIS 0.014 0.002 HIS B 275 PHE 0.020 0.002 PHE B 162 TYR 0.021 0.002 TYR A 625 ARG 0.006 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: D 582 MET cc_start: 0.6617 (ppp) cc_final: 0.6183 (ppp) REVERT: E 130 LEU cc_start: 0.9661 (tp) cc_final: 0.9422 (tp) REVERT: E 226 PHE cc_start: 0.8438 (m-80) cc_final: 0.8004 (m-80) REVERT: E 357 MET cc_start: 0.8879 (mtm) cc_final: 0.8294 (mtm) REVERT: E 455 LEU cc_start: 0.9238 (mp) cc_final: 0.8626 (mp) REVERT: A 339 MET cc_start: 0.7985 (ppp) cc_final: 0.7727 (ppp) REVERT: A 508 MET cc_start: 0.7949 (mpp) cc_final: 0.7707 (mpp) REVERT: B 288 LEU cc_start: 0.8267 (mp) cc_final: 0.7695 (mp) REVERT: B 340 ASP cc_start: 0.6476 (m-30) cc_final: 0.6119 (m-30) REVERT: B 357 MET cc_start: 0.8012 (mpp) cc_final: 0.7649 (mpp) REVERT: B 463 MET cc_start: 0.8638 (ptp) cc_final: 0.7351 (mpp) REVERT: B 636 MET cc_start: 0.8719 (tpt) cc_final: 0.8516 (tpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2646 time to fit residues: 36.2480 Evaluate side-chains 65 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18574 Z= 0.226 Angle : 0.631 11.091 25248 Z= 0.322 Chirality : 0.047 0.395 2804 Planarity : 0.004 0.048 3256 Dihedral : 8.326 82.287 2629 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.39 (0.17), residues: 2291 helix: -1.08 (0.42), residues: 153 sheet: -0.51 (0.22), residues: 522 loop : -1.09 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 428 HIS 0.011 0.001 HIS B 275 PHE 0.042 0.002 PHE E 374 TYR 0.014 0.002 TYR A 625 ARG 0.005 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.168 Fit side-chains revert: symmetry clash REVERT: D 508 MET cc_start: 0.6555 (tpt) cc_final: 0.6314 (tpt) REVERT: D 582 MET cc_start: 0.6972 (ppp) cc_final: 0.6510 (ppp) REVERT: E 130 LEU cc_start: 0.9668 (tp) cc_final: 0.9433 (tp) REVERT: E 226 PHE cc_start: 0.8377 (m-80) cc_final: 0.8121 (m-80) REVERT: E 357 MET cc_start: 0.8865 (mtm) cc_final: 0.8347 (mtm) REVERT: A 339 MET cc_start: 0.7907 (ppp) cc_final: 0.7644 (ppp) REVERT: B 288 LEU cc_start: 0.8285 (mp) cc_final: 0.7723 (mp) REVERT: B 340 ASP cc_start: 0.6527 (m-30) cc_final: 0.6134 (m-30) REVERT: B 357 MET cc_start: 0.7992 (mpp) cc_final: 0.7707 (mpp) REVERT: B 463 MET cc_start: 0.8696 (ptp) cc_final: 0.7269 (mpp) REVERT: B 583 ILE cc_start: 0.8502 (mm) cc_final: 0.8160 (mp) REVERT: B 636 MET cc_start: 0.8660 (tpt) cc_final: 0.8460 (tpp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2547 time to fit residues: 35.6390 Evaluate side-chains 64 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 9.9990 chunk 218 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18574 Z= 0.194 Angle : 0.608 9.048 25248 Z= 0.308 Chirality : 0.046 0.346 2804 Planarity : 0.004 0.047 3256 Dihedral : 7.961 77.132 2629 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.32 (0.18), residues: 2291 helix: -0.90 (0.42), residues: 158 sheet: -0.39 (0.23), residues: 509 loop : -1.08 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 617 HIS 0.009 0.001 HIS B 275 PHE 0.016 0.002 PHE A 190 TYR 0.014 0.001 TYR B 41 ARG 0.004 0.000 ARG B 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.253 Fit side-chains revert: symmetry clash REVERT: D 508 MET cc_start: 0.6484 (tpt) cc_final: 0.6258 (tpt) REVERT: D 637 MET cc_start: 0.7116 (mmt) cc_final: 0.6562 (mmt) REVERT: E 35 MET cc_start: 0.6967 (tmm) cc_final: 0.6599 (tmm) REVERT: E 39 MET cc_start: 0.5938 (mpp) cc_final: 0.5532 (mmm) REVERT: E 130 LEU cc_start: 0.9669 (tp) cc_final: 0.9445 (tp) REVERT: E 294 MET cc_start: 0.8811 (tpp) cc_final: 0.8570 (tpp) REVERT: E 357 MET cc_start: 0.8831 (mtm) cc_final: 0.8314 (mtm) REVERT: A 339 MET cc_start: 0.7917 (ppp) cc_final: 0.7651 (ppp) REVERT: B 288 LEU cc_start: 0.8375 (mp) cc_final: 0.7843 (mp) REVERT: B 340 ASP cc_start: 0.6501 (m-30) cc_final: 0.6119 (m-30) REVERT: B 357 MET cc_start: 0.7972 (mpp) cc_final: 0.7708 (mpp) REVERT: B 463 MET cc_start: 0.8584 (ptp) cc_final: 0.7377 (mpp) REVERT: B 583 ILE cc_start: 0.8456 (mm) cc_final: 0.8141 (mp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2605 time to fit residues: 36.9505 Evaluate side-chains 67 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 168 optimal weight: 0.0570 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 182 optimal weight: 0.0770 chunk 76 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 33 optimal weight: 0.4980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 115 ASN B 289 HIS ** B 382 ASN ** 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 = 0.3292 r_free = 0.3292 target = 0.036500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.027858 restraints weight = 277227.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.028517 restraints weight = 181808.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.029052 restraints weight = 136199.521| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18574 Z= 0.154 Angle : 0.594 8.651 25248 Z= 0.296 Chirality : 0.046 0.330 2804 Planarity : 0.004 0.048 3256 Dihedral : 7.399 69.134 2629 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.17 (0.17), residues: 2291 helix: -0.81 (0.41), residues: 165 sheet: -0.16 (0.23), residues: 492 loop : -1.01 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 617 HIS 0.006 0.001 HIS B 275 PHE 0.035 0.001 PHE E 374 TYR 0.013 0.001 TYR E 369 ARG 0.004 0.000 ARG B 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.81 seconds wall clock time: 49 minutes 3.06 seconds (2943.06 seconds total)