Starting phenix.real_space_refine on Sat Feb 17 03:12:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvg_30219/02_2024/7bvg_30219_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.060 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 7 5.49 5 S 60 5.16 5 C 11116 2.51 5 N 2919 2.21 5 O 3127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A ARG 886": "NH1" <-> "NH2" Residue "A ASP 888": "OD1" <-> "OD2" Residue "A TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A ARG 926": "NH1" <-> "NH2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A ARG 1033": "NH1" <-> "NH2" Residue "A GLU 1044": "OE1" <-> "OE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 681": "NH1" <-> "NH2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B ASP 765": "OD1" <-> "OD2" Residue "B ASP 776": "OD1" <-> "OD2" Residue "B ARG 777": "NH1" <-> "NH2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 822": "NH1" <-> "NH2" Residue "B ARG 849": "NH1" <-> "NH2" Residue "B ASP 850": "OD1" <-> "OD2" Residue "B ARG 890": "NH1" <-> "NH2" Residue "B ASP 925": "OD1" <-> "OD2" Residue "B ARG 931": "NH1" <-> "NH2" Residue "B GLU 935": "OE1" <-> "OE2" Residue "B ASP 943": "OD1" <-> "OD2" Residue "B ARG 951": "NH1" <-> "NH2" Residue "B ARG 997": "NH1" <-> "NH2" Residue "B ASP 1025": "OD1" <-> "OD2" Residue "B ASP 1040": "OD1" <-> "OD2" Residue "B ASP 1044": "OD1" <-> "OD2" Residue "B TYR 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1079": "NH1" <-> "NH2" Residue "P GLU 14": "OE1" <-> "OE2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ASP 38": "OD1" <-> "OD2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "P ASP 63": "OD1" <-> "OD2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17231 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8147 Classifications: {'peptide': 1078} Link IDs: {'PCIS': 1, 'PTRANS': 78, 'TRANS': 998} Chain: "B" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8105 Classifications: {'peptide': 1063} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 985} Chain: "P" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 706 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'BXY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {' CA': 1, 'CDL': 1, 'F8L': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'F8L:plan-4': 1, 'F8L:plan-2': 1, 'F8L:plan-1': 1, 'F8L:plan-10': 1, 'F8L:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Unusual residues: {' CA': 1, 'CDL': 1, 'PNS': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.09, per 1000 atoms: 0.59 Number of scatterers: 17231 At special positions: 0 Unit cell: (123, 133.66, 122.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 60 16.00 P 7 15.00 O 3127 8.00 N 2919 7.00 C 11116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Links applied ALPHA1-5 " BXY C 1 " - " BXY C 2 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.47 Conformation dependent library (CDL) restraints added in 3.5 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 14 sheets defined 34.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 removed outlier: 3.739A pdb=" N VAL A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 123 through 126 No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 196 through 222 removed outlier: 3.731A pdb=" N VAL A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 removed outlier: 3.769A pdb=" N THR A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 270 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 296 through 302 removed outlier: 4.082A pdb=" N HIS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.660A pdb=" N ALA A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 335 No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.122A pdb=" N LEU A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 4.017A pdb=" N PHE A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 404 removed outlier: 4.040A pdb=" N ILE A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.942A pdb=" N LEU A 411 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 442 through 454 removed outlier: 4.100A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 removed outlier: 3.553A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.570A pdb=" N LEU A 490 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 522 removed outlier: 3.757A pdb=" N ALA A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 549 removed outlier: 3.703A pdb=" N TRP A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 582 removed outlier: 3.881A pdb=" N PHE A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 560 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY A 564 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 566 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY A 567 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 571 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 573 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA A 574 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N PHE A 577 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 578 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 581 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 582 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 604 removed outlier: 3.661A pdb=" N ALA A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 651 removed outlier: 3.645A pdb=" N VAL A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 677 through 695 removed outlier: 4.533A pdb=" N MET A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.962A pdb=" N ASN A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 997 through 1003 removed outlier: 3.558A pdb=" N VAL A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 removed outlier: 3.799A pdb=" N TRP B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 39 No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 231 through 247 removed outlier: 4.474A pdb=" N ALA B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 removed outlier: 3.708A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 279 No H-bonds generated for 'chain 'B' and resid 276 through 279' Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 320 through 328 removed outlier: 3.759A pdb=" N LEU B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.519A pdb=" N CYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 391 through 411 removed outlier: 3.559A pdb=" N THR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 428 removed outlier: 3.850A pdb=" N LEU B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 420 " --> pdb=" O PRO B 416 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.746A pdb=" N ALA B 440 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 443 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.605A pdb=" N ILE B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 474 Proline residue: B 467 - end of helix removed outlier: 3.561A pdb=" N GLY B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'B' and resid 485 through 498 Processing helix chain 'B' and resid 504 through 515 removed outlier: 3.505A pdb=" N GLU B 507 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASN B 508 " --> pdb=" O TRP B 505 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 509 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR B 513 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 545 removed outlier: 4.059A pdb=" N THR B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Proline residue: B 538 - end of helix removed outlier: 3.533A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 570 removed outlier: 3.538A pdb=" N MET B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 599 removed outlier: 3.992A pdb=" N LEU B 584 " --> pdb=" O HIS B 581 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 585 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 587 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 589 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 590 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA B 591 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 597 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 625 Processing helix chain 'B' and resid 655 through 674 Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 690 through 712 removed outlier: 3.783A pdb=" N MET B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 removed outlier: 3.972A pdb=" N PHE B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 728 " --> pdb=" O ILE B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 961 No H-bonds generated for 'chain 'B' and resid 958 through 961' Processing helix chain 'B' and resid 1002 through 1005 No H-bonds generated for 'chain 'B' and resid 1002 through 1005' Processing helix chain 'B' and resid 1015 through 1017 No H-bonds generated for 'chain 'B' and resid 1015 through 1017' Processing helix chain 'B' and resid 1020 through 1022 No H-bonds generated for 'chain 'B' and resid 1020 through 1022' Processing helix chain 'P' and resid 5 through 19 removed outlier: 3.748A pdb=" N ALA P 10 " --> pdb=" O GLU P 6 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU P 14 " --> pdb=" O ALA P 10 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 54 removed outlier: 3.856A pdb=" N GLU P 46 " --> pdb=" O LEU P 42 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP P 53 " --> pdb=" O VAL P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 66 removed outlier: 3.935A pdb=" N ALA P 65 " --> pdb=" O ASP P 61 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY P 66 " --> pdb=" O GLU P 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 66' Processing helix chain 'P' and resid 70 through 82 Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 4.103A pdb=" N ALA A 182 " --> pdb=" O TRP A 40 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 64 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 825 through 827 removed outlier: 3.694A pdb=" N MET A 826 " --> pdb=" O PHE A 942 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 837 through 839 removed outlier: 3.500A pdb=" N VAL A 928 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 879 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 877 " --> pdb=" O ASP A 930 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 855 through 858 Processing sheet with id= E, first strand: chain 'A' and resid 963 through 965 removed outlier: 6.857A pdb=" N TYR A 991 " --> pdb=" O LEU A 964 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A1043 " --> pdb=" O ILE A1028 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 216 through 218 Processing sheet with id= G, first strand: chain 'B' and resid 82 through 84 Processing sheet with id= H, first strand: chain 'B' and resid 125 through 127 removed outlier: 4.149A pdb=" N PHE B 99 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.802A pdb=" N THR B 178 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 1035 through 1037 Processing sheet with id= K, first strand: chain 'B' and resid 826 through 828 removed outlier: 3.957A pdb=" N ILE B 945 " --> pdb=" O THR B 828 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 865 " --> pdb=" O ALA B 946 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 838 through 840 Processing sheet with id= M, first strand: chain 'B' and resid 929 through 932 removed outlier: 3.794A pdb=" N ALA B 929 " --> pdb=" O ALA B 888 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 889 " --> pdb=" O VAL B 897 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 891 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 968 through 970 removed outlier: 6.797A pdb=" N PHE B 996 " --> pdb=" O LEU B 969 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.91 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2755 1.29 - 1.42: 4467 1.42 - 1.55: 10316 1.55 - 1.69: 19 1.69 - 1.82: 102 Bond restraints: 17659 Sorted by residual: bond pdb=" C2 BXY C 2 " pdb=" C3 BXY C 2 " ideal model delta sigma weight residual 1.518 1.220 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C1 BXY C 1 " pdb=" C2 BXY C 1 " ideal model delta sigma weight residual 1.525 1.254 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C1 BXY C 1 " pdb=" O4 BXY C 1 " ideal model delta sigma weight residual 1.412 1.653 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C61 F8L A1101 " pdb=" O56 F8L A1101 " ideal model delta sigma weight residual 1.272 1.509 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C59 F8L A1101 " pdb=" C61 F8L A1101 " ideal model delta sigma weight residual 1.568 1.345 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 17654 not shown) Histogram of bond angle deviations from ideal: 94.54 - 102.61: 101 102.61 - 110.67: 5971 110.67 - 118.74: 8331 118.74 - 126.81: 9386 126.81 - 134.88: 357 Bond angle restraints: 24146 Sorted by residual: angle pdb=" C46 F8L A1101 " pdb=" C47 F8L A1101 " pdb=" C48 F8L A1101 " ideal model delta sigma weight residual 74.51 125.39 -50.88 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C31 F8L A1101 " pdb=" C32 F8L A1101 " pdb=" C33 F8L A1101 " ideal model delta sigma weight residual 74.51 121.12 -46.61 3.00e+00 1.11e-01 2.41e+02 angle pdb=" C26 F8L A1101 " pdb=" C27 F8L A1101 " pdb=" C28 F8L A1101 " ideal model delta sigma weight residual 74.52 119.81 -45.29 3.00e+00 1.11e-01 2.28e+02 angle pdb=" C36 F8L A1101 " pdb=" C37 F8L A1101 " pdb=" C38 F8L A1101 " ideal model delta sigma weight residual 74.50 117.36 -42.86 3.00e+00 1.11e-01 2.04e+02 angle pdb=" C41 F8L A1101 " pdb=" C42 F8L A1101 " pdb=" C43 F8L A1101 " ideal model delta sigma weight residual 74.51 117.32 -42.81 3.00e+00 1.11e-01 2.04e+02 ... (remaining 24141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 10113 29.86 - 59.71: 331 59.71 - 89.57: 21 89.57 - 119.43: 2 119.43 - 149.29: 3 Dihedral angle restraints: 10470 sinusoidal: 4112 harmonic: 6358 Sorted by residual: dihedral pdb=" CA TRP A 40 " pdb=" C TRP A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta harmonic sigma weight residual -180.00 -62.36 -117.64 0 5.00e+00 4.00e-02 5.54e+02 dihedral pdb=" CA TRP B 58 " pdb=" C TRP B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta harmonic sigma weight residual 180.00 82.70 97.30 0 5.00e+00 4.00e-02 3.79e+02 dihedral pdb=" N THR B 716 " pdb=" C THR B 716 " pdb=" CA THR B 716 " pdb=" CB THR B 716 " ideal model delta harmonic sigma weight residual 123.40 142.08 -18.68 0 2.50e+00 1.60e-01 5.58e+01 ... (remaining 10467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2750 0.146 - 0.291: 14 0.291 - 0.437: 3 0.437 - 0.583: 1 0.583 - 0.728: 1 Chirality restraints: 2769 Sorted by residual: chirality pdb=" CA THR B 716 " pdb=" N THR B 716 " pdb=" C THR B 716 " pdb=" CB THR B 716 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 BXY C 2 " pdb=" O5 BXY C 1 " pdb=" C2 BXY C 2 " pdb=" O4 BXY C 2 " both_signs ideal model delta sigma weight residual False 2.60 2.54 0.06 2.00e-02 2.50e+03 7.88e+00 chirality pdb=" CA PRO A 41 " pdb=" N PRO A 41 " pdb=" C PRO A 41 " pdb=" CB PRO A 41 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.12e+00 ... (remaining 2766 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1079 " 0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO A1080 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A1080 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1080 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 58 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C TRP B 58 " 0.068 2.00e-02 2.50e+03 pdb=" O TRP B 58 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 59 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 910 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.92e+00 pdb=" N PRO B 911 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 911 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 911 " 0.043 5.00e-02 4.00e+02 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 68 2.43 - 3.05: 10887 3.05 - 3.67: 24878 3.67 - 4.28: 38150 4.28 - 4.90: 65259 Nonbonded interactions: 139242 Sorted by model distance: nonbonded pdb=" OG SER P 41 " pdb=" O25 PNS B1202 " model vdw 1.815 2.440 nonbonded pdb=" OG SER P 41 " pdb=" O23 PNS B1202 " model vdw 1.937 2.440 nonbonded pdb=" CB SER P 41 " pdb=" O25 PNS B1202 " model vdw 1.961 3.440 nonbonded pdb=" O PRO A 699 " pdb=" N TYR A 701 " model vdw 2.143 2.520 nonbonded pdb=" N ASN B 57 " pdb=" OD1 ASN B 57 " model vdw 2.166 2.520 ... (remaining 139237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.660 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: 10.500 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 52.170 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.298 17659 Z= 0.480 Angle : 1.139 50.878 24146 Z= 0.568 Chirality : 0.051 0.728 2769 Planarity : 0.006 0.099 3086 Dihedral : 14.687 149.285 6404 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.57 % Favored : 91.11 % Rotamer: Outliers : 0.17 % Allowed : 4.15 % Favored : 95.67 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -4.51 (0.15), residues: 2228 helix: -2.53 (0.15), residues: 839 sheet: -2.69 (0.32), residues: 218 loop : -3.50 (0.15), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 324 HIS 0.002 0.001 HIS B 857 PHE 0.012 0.001 PHE A 942 TYR 0.039 0.002 TYR B 714 ARG 0.004 0.000 ARG B 914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 248 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PRO cc_start: 0.8529 (OUTLIER) cc_final: 0.8312 (Cg_exo) REVERT: B 21 LYS cc_start: 0.7286 (tptt) cc_final: 0.7074 (ttpp) REVERT: B 273 MET cc_start: 0.7330 (tpt) cc_final: 0.6968 (tpp) REVERT: P 63 ASP cc_start: 0.8051 (t70) cc_final: 0.7766 (t0) outliers start: 3 outliers final: 2 residues processed: 251 average time/residue: 0.3707 time to fit residues: 131.9821 Evaluate side-chains 180 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PRO Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain B residue 57 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 174 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 201 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 361 ASN A 482 GLN A 650 HIS A1008 GLN B 291 GLN B 393 GLN B 431 GLN B 502 GLN B 508 ASN B 610 ASN B 630 ASN B 653 GLN B 719 ASN B 959 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17659 Z= 0.190 Angle : 0.800 23.705 24146 Z= 0.347 Chirality : 0.043 0.158 2769 Planarity : 0.006 0.115 3086 Dihedral : 11.306 124.498 2681 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.89 % Favored : 90.93 % Rotamer: Outliers : 1.37 % Allowed : 9.85 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -3.67 (0.16), residues: 2228 helix: -1.74 (0.17), residues: 838 sheet: -2.32 (0.32), residues: 228 loop : -3.07 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 843 HIS 0.005 0.001 HIS B 673 PHE 0.017 0.001 PHE A 979 TYR 0.016 0.001 TYR B 844 ARG 0.007 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 2.114 Fit side-chains REVERT: A 947 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 957 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8675 (pp) REVERT: B 801 LYS cc_start: 0.7940 (mttp) cc_final: 0.7576 (ttmm) REVERT: P 63 ASP cc_start: 0.8002 (t70) cc_final: 0.7699 (t0) outliers start: 24 outliers final: 17 residues processed: 207 average time/residue: 0.3291 time to fit residues: 100.9522 Evaluate side-chains 187 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 775 ASN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 1016 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 0.3980 chunk 218 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 200 optimal weight: 0.0020 chunk 68 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN B 719 ASN B 767 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17659 Z= 0.166 Angle : 0.774 23.168 24146 Z= 0.332 Chirality : 0.042 0.154 2769 Planarity : 0.005 0.133 3086 Dihedral : 10.648 117.903 2675 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.75 % Favored : 91.16 % Rotamer: Outliers : 1.71 % Allowed : 12.01 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -3.12 (0.17), residues: 2228 helix: -1.19 (0.18), residues: 821 sheet: -1.95 (0.34), residues: 219 loop : -2.83 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 843 HIS 0.002 0.001 HIS B 217 PHE 0.013 0.001 PHE A 979 TYR 0.015 0.001 TYR A 891 ARG 0.014 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.933 Fit side-chains REVERT: A 947 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8603 (p) REVERT: A 957 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8624 (pp) REVERT: P 63 ASP cc_start: 0.8010 (t70) cc_final: 0.7706 (t0) outliers start: 30 outliers final: 15 residues processed: 201 average time/residue: 0.3252 time to fit residues: 98.0345 Evaluate side-chains 178 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 775 ASN Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 719 ASN Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 1016 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 202 optimal weight: 0.4980 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 0.0040 chunk 192 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1008 GLN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17659 Z= 0.157 Angle : 0.760 22.776 24146 Z= 0.322 Chirality : 0.042 0.149 2769 Planarity : 0.006 0.142 3086 Dihedral : 10.201 113.144 2673 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.57 % Favored : 91.34 % Rotamer: Outliers : 1.54 % Allowed : 13.38 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.79 (0.17), residues: 2228 helix: -0.90 (0.18), residues: 819 sheet: -1.83 (0.34), residues: 218 loop : -2.62 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 843 HIS 0.002 0.000 HIS B 217 PHE 0.011 0.001 PHE A 942 TYR 0.015 0.001 TYR A 746 ARG 0.007 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.773 Fit side-chains REVERT: A 137 TRP cc_start: 0.7960 (p90) cc_final: 0.7420 (p90) REVERT: A 947 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8578 (p) REVERT: A 957 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8592 (pp) REVERT: B 821 LYS cc_start: 0.8449 (mptt) cc_final: 0.8205 (mmtp) REVERT: P 63 ASP cc_start: 0.8000 (t70) cc_final: 0.7705 (t0) outliers start: 27 outliers final: 16 residues processed: 193 average time/residue: 0.3169 time to fit residues: 91.4845 Evaluate side-chains 177 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1016 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 623 GLN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17659 Z= 0.244 Angle : 0.788 22.629 24146 Z= 0.339 Chirality : 0.043 0.166 2769 Planarity : 0.006 0.146 3086 Dihedral : 9.959 107.346 2673 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.35 % Rotamer: Outliers : 1.71 % Allowed : 14.68 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.67 (0.17), residues: 2228 helix: -0.86 (0.18), residues: 830 sheet: -1.86 (0.34), residues: 225 loop : -2.49 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 843 HIS 0.003 0.001 HIS B 217 PHE 0.013 0.001 PHE B 99 TYR 0.016 0.001 TYR A 746 ARG 0.008 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 2.200 Fit side-chains REVERT: A 947 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 957 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (pp) REVERT: P 63 ASP cc_start: 0.8001 (t70) cc_final: 0.7680 (t0) outliers start: 30 outliers final: 19 residues processed: 194 average time/residue: 0.3071 time to fit residues: 89.8407 Evaluate side-chains 183 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1016 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 71 optimal weight: 0.0570 chunk 112 optimal weight: 0.0000 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 719 ASN ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 17659 Z= 0.138 Angle : 0.754 22.389 24146 Z= 0.318 Chirality : 0.041 0.158 2769 Planarity : 0.005 0.149 3086 Dihedral : 9.240 100.698 2673 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.41 % Rotamer: Outliers : 1.88 % Allowed : 14.97 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.30 (0.17), residues: 2228 helix: -0.48 (0.19), residues: 812 sheet: -1.75 (0.34), residues: 229 loop : -2.29 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 843 HIS 0.003 0.000 HIS A 135 PHE 0.011 0.001 PHE A 979 TYR 0.015 0.001 TYR A 829 ARG 0.006 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.796 Fit side-chains REVERT: A 137 TRP cc_start: 0.7969 (p90) cc_final: 0.7447 (p90) REVERT: A 869 ASP cc_start: 0.8484 (p0) cc_final: 0.8245 (p0) REVERT: A 947 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8563 (p) REVERT: P 63 ASP cc_start: 0.7999 (t70) cc_final: 0.7689 (t0) outliers start: 33 outliers final: 19 residues processed: 204 average time/residue: 0.3135 time to fit residues: 96.0239 Evaluate side-chains 188 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 719 ASN Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1068 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 133 optimal weight: 0.0270 chunk 130 optimal weight: 0.0050 chunk 98 optimal weight: 2.9990 overall best weight: 1.0054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 ASN ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17659 Z= 0.201 Angle : 0.768 22.449 24146 Z= 0.326 Chirality : 0.042 0.164 2769 Planarity : 0.005 0.150 3086 Dihedral : 9.012 95.079 2673 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 1.42 % Allowed : 16.11 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.24 (0.17), residues: 2228 helix: -0.52 (0.19), residues: 825 sheet: -1.56 (0.34), residues: 234 loop : -2.24 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 843 HIS 0.003 0.001 HIS A 135 PHE 0.013 0.001 PHE B 99 TYR 0.015 0.001 TYR A 829 ARG 0.007 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 2.063 Fit side-chains REVERT: A 869 ASP cc_start: 0.8468 (p0) cc_final: 0.8239 (p0) REVERT: A 947 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8579 (p) REVERT: B 543 MET cc_start: 0.8386 (mmm) cc_final: 0.8065 (mtp) REVERT: P 63 ASP cc_start: 0.8012 (t70) cc_final: 0.7688 (t0) outliers start: 25 outliers final: 22 residues processed: 187 average time/residue: 0.3182 time to fit residues: 89.5006 Evaluate side-chains 185 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 719 ASN Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1016 ILE Chi-restraints excluded: chain B residue 1068 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 0.0270 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 0.0170 chunk 19 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17659 Z= 0.145 Angle : 0.754 22.297 24146 Z= 0.318 Chirality : 0.041 0.161 2769 Planarity : 0.005 0.150 3086 Dihedral : 8.678 89.914 2673 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.45 % Favored : 92.46 % Rotamer: Outliers : 1.59 % Allowed : 16.33 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.03 (0.18), residues: 2228 helix: -0.30 (0.19), residues: 819 sheet: -1.48 (0.34), residues: 234 loop : -2.14 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 843 HIS 0.003 0.000 HIS A 135 PHE 0.010 0.001 PHE A 942 TYR 0.014 0.001 TYR A 829 ARG 0.008 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 2.003 Fit side-chains REVERT: A 137 TRP cc_start: 0.8004 (p90) cc_final: 0.7537 (p90) REVERT: A 947 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 543 MET cc_start: 0.8406 (mmm) cc_final: 0.8104 (mtp) REVERT: P 63 ASP cc_start: 0.7991 (t70) cc_final: 0.7670 (t0) outliers start: 28 outliers final: 21 residues processed: 189 average time/residue: 0.3117 time to fit residues: 89.3405 Evaluate side-chains 187 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1068 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 9.9990 chunk 204 optimal weight: 0.0970 chunk 187 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17659 Z= 0.199 Angle : 0.773 22.291 24146 Z= 0.330 Chirality : 0.043 0.165 2769 Planarity : 0.005 0.151 3086 Dihedral : 8.631 85.602 2673 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.74 % Rotamer: Outliers : 1.71 % Allowed : 16.51 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.02 (0.18), residues: 2228 helix: -0.32 (0.19), residues: 818 sheet: -1.44 (0.35), residues: 232 loop : -2.11 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 843 HIS 0.003 0.001 HIS A 135 PHE 0.013 0.001 PHE B 99 TYR 0.014 0.001 TYR A 746 ARG 0.008 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 2.171 Fit side-chains REVERT: A 787 LYS cc_start: 0.8622 (ptpp) cc_final: 0.8287 (ptpp) REVERT: A 947 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8552 (p) REVERT: B 543 MET cc_start: 0.8397 (mmm) cc_final: 0.8113 (mtp) REVERT: P 63 ASP cc_start: 0.7978 (t70) cc_final: 0.7663 (t0) outliers start: 30 outliers final: 27 residues processed: 191 average time/residue: 0.3182 time to fit residues: 91.6140 Evaluate side-chains 194 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1016 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 128 optimal weight: 0.0070 chunk 100 optimal weight: 0.0770 chunk 146 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17659 Z= 0.143 Angle : 0.756 22.113 24146 Z= 0.319 Chirality : 0.041 0.174 2769 Planarity : 0.005 0.151 3086 Dihedral : 8.238 81.707 2673 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 1.54 % Allowed : 16.79 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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 (0.18), residues: 2228 helix: -0.09 (0.19), residues: 817 sheet: -1.33 (0.36), residues: 219 loop : -2.06 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 843 HIS 0.004 0.001 HIS A 135 PHE 0.011 0.001 PHE A 942 TYR 0.014 0.001 TYR A 829 ARG 0.008 0.000 ARG A 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 137 TRP cc_start: 0.8020 (p90) cc_final: 0.7638 (p90) REVERT: A 837 LYS cc_start: 0.7614 (tptt) cc_final: 0.7232 (tptp) REVERT: B 543 MET cc_start: 0.8376 (mmm) cc_final: 0.8077 (mtp) REVERT: P 63 ASP cc_start: 0.7962 (t70) cc_final: 0.7590 (t0) outliers start: 27 outliers final: 25 residues processed: 191 average time/residue: 0.3033 time to fit residues: 87.8823 Evaluate side-chains 190 residues out of total 1757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 0.0470 chunk 73 optimal weight: 8.9990 chunk 181 optimal weight: 0.0970 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106771 restraints weight = 24887.773| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.13 r_work: 0.3235 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 17659 Z= 0.148 Angle : 0.758 22.106 24146 Z= 0.320 Chirality : 0.042 0.200 2769 Planarity : 0.005 0.151 3086 Dihedral : 8.102 80.960 2673 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.54 % Favored : 92.37 % Rotamer: Outliers : 1.59 % Allowed : 16.79 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -1.71 (0.18), residues: 2228 helix: 0.01 (0.19), residues: 816 sheet: -1.33 (0.36), residues: 231 loop : -1.97 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 843 HIS 0.003 0.000 HIS A 135 PHE 0.011 0.001 PHE A 942 TYR 0.014 0.001 TYR A 829 ARG 0.008 0.000 ARG A 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3973.79 seconds wall clock time: 72 minutes 39.11 seconds (4359.11 seconds total)