Starting phenix.real_space_refine on Thu Feb 15 23:16:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/02_2024/7d90_30616.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/02_2024/7d90_30616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/02_2024/7d90_30616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/02_2024/7d90_30616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/02_2024/7d90_30616.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/02_2024/7d90_30616.pdb" } resolution = 3.6 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= 0.003 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 98 5.16 5 C 8910 2.51 5 N 2266 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A TYR 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ARG 937": "NH1" <-> "NH2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 593": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B TYR 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 731": "NH1" <-> "NH2" Residue "B ARG 739": "NH1" <-> "NH2" Residue "B ARG 937": "NH1" <-> "NH2" Residue "B ARG 1113": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13686 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6815 Classifications: {'peptide': 880} Link IDs: {'PTRANS': 32, 'TRANS': 847} Chain breaks: 1 Chain: "B" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6815 Classifications: {'peptide': 880} Link IDs: {'PTRANS': 32, 'TRANS': 847} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.49, per 1000 atoms: 0.55 Number of scatterers: 13686 At special positions: 0 Unit cell: (108.498, 114.582, 150.072, 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 98 16.00 O 2412 8.00 N 2266 7.00 C 8910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 653 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 653 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 420 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A 379 " " NAG A1202 " - " ASN A 428 " " NAG B1201 " - " ASN B 379 " " NAG B1202 " - " ASN B 428 " Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 2.7 seconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 6 sheets defined 59.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.509A pdb=" N TYR A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.514A pdb=" N ASN A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.508A pdb=" N ARG A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 244 removed outlier: 3.680A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 233 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 234 " --> pdb=" O CYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.598A pdb=" N ALA A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 294 removed outlier: 3.752A pdb=" N GLY A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 335 removed outlier: 3.660A pdb=" N VAL A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.611A pdb=" N VAL A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 366 removed outlier: 3.578A pdb=" N PHE A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 354 " --> pdb=" O CYS A 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.531A pdb=" N GLY A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.917A pdb=" N HIS A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 removed outlier: 3.508A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 498 through 504 removed outlier: 3.859A pdb=" N SER A 503 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 504 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 540 Proline residue: A 517 - end of helix removed outlier: 3.702A pdb=" N THR A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 549 through 553 removed outlier: 4.096A pdb=" N GLY A 552 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 553 " --> pdb=" O LYS A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 568 through 600 removed outlier: 3.997A pdb=" N ILE A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix removed outlier: 3.733A pdb=" N GLN A 596 " --> pdb=" O PRO A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.634A pdb=" N ARG A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL A 609 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 610 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.944A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 667 Proline residue: A 644 - end of helix removed outlier: 3.601A pdb=" N PHE A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 699 removed outlier: 4.019A pdb=" N SER A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 726 removed outlier: 4.050A pdb=" N VAL A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 724 " --> pdb=" O GLN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 743 removed outlier: 4.039A pdb=" N SER A 734 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 782 removed outlier: 3.686A pdb=" N SER A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 819 removed outlier: 3.962A pdb=" N GLN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 845 removed outlier: 3.733A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 844 " --> pdb=" O SER A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 886 removed outlier: 3.707A pdb=" N VAL A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.552A pdb=" N PHE A 899 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 932 Proline residue: A 927 - end of helix removed outlier: 3.542A pdb=" N LYS A 931 " --> pdb=" O PRO A 927 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 932 " --> pdb=" O PHE A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 967 Processing helix chain 'A' and resid 983 through 993 removed outlier: 4.435A pdb=" N GLU A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1099 removed outlier: 3.819A pdb=" N THR A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A1088 " --> pdb=" O MET A1084 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1129 removed outlier: 3.564A pdb=" N MET A1122 " --> pdb=" O ASP A1118 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE A1124 " --> pdb=" O ASN A1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.509A pdb=" N TYR B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.514A pdb=" N ASN B 198 " --> pdb=" O PRO B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 removed outlier: 3.508A pdb=" N ARG B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 244 removed outlier: 3.680A pdb=" N VAL B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 225 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 233 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 234 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.598A pdb=" N ALA B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 294 removed outlier: 3.752A pdb=" N GLY B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 335 removed outlier: 3.660A pdb=" N VAL B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 322 " --> pdb=" O MET B 318 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.611A pdb=" N VAL B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 366 removed outlier: 3.578A pdb=" N PHE B 347 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 354 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.531A pdb=" N GLY B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.917A pdb=" N HIS B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 removed outlier: 3.508A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 498 through 504 removed outlier: 3.859A pdb=" N SER B 503 " --> pdb=" O MET B 500 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 504 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 511 through 540 Proline residue: B 517 - end of helix removed outlier: 3.702A pdb=" N THR B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 521 " --> pdb=" O PRO B 517 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 523 " --> pdb=" O GLY B 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 549 through 553 removed outlier: 4.096A pdb=" N GLY B 552 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 553 " --> pdb=" O LYS B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 553' Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 568 through 600 removed outlier: 3.997A pdb=" N ILE B 572 " --> pdb=" O SER B 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 590 " --> pdb=" O GLN B 586 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 3.738A pdb=" N GLN B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.634A pdb=" N ARG B 608 " --> pdb=" O PRO B 605 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL B 609 " --> pdb=" O PHE B 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 610 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS B 612 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 635 removed outlier: 3.944A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 667 Proline residue: B 644 - end of helix removed outlier: 3.601A pdb=" N PHE B 649 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 4.019A pdb=" N SER B 684 " --> pdb=" O HIS B 680 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 699 " --> pdb=" O MET B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 726 removed outlier: 4.050A pdb=" N VAL B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 722 " --> pdb=" O GLU B 718 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 743 removed outlier: 4.039A pdb=" N SER B 734 " --> pdb=" O ILE B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 782 removed outlier: 3.686A pdb=" N SER B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 819 removed outlier: 3.962A pdb=" N GLN B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 813 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 845 removed outlier: 3.733A pdb=" N ILE B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 844 " --> pdb=" O SER B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 886 removed outlier: 3.707A pdb=" N VAL B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 882 " --> pdb=" O GLY B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.552A pdb=" N PHE B 899 " --> pdb=" O ILE B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 932 Proline residue: B 927 - end of helix removed outlier: 3.542A pdb=" N LYS B 931 " --> pdb=" O PRO B 927 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN B 932 " --> pdb=" O PHE B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 967 Processing helix chain 'B' and resid 983 through 993 removed outlier: 4.435A pdb=" N GLU B 989 " --> pdb=" O ALA B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1099 removed outlier: 3.819A pdb=" N THR B1086 " --> pdb=" O ARG B1082 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B1088 " --> pdb=" O MET B1084 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B1089 " --> pdb=" O HIS B1085 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B1093 " --> pdb=" O LYS B1089 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B1097 " --> pdb=" O VAL B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1117 through 1129 removed outlier: 3.564A pdb=" N MET B1122 " --> pdb=" O ASP B1118 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE B1124 " --> pdb=" O ASN B1120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 376 Processing sheet with id=AA2, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA3, first strand: chain 'A' and resid 826 through 832 removed outlier: 6.530A pdb=" N THR A 790 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLN A 828 " --> pdb=" O THR A 790 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 792 " --> pdb=" O GLN A 828 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL A 830 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER A 794 " --> pdb=" O VAL A 830 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA A 832 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE A 796 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 760 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 856 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA A 893 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET A 858 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A1135 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU A1136 " --> pdb=" O LYS A1102 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A1104 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A1138 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A1106 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N GLU A 908 " --> pdb=" O ALA A1101 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU A1103 " --> pdb=" O GLU A 908 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN A 910 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU A1105 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP A 912 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN A1107 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 907 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER A 940 " --> pdb=" O SER A 907 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY A 909 " --> pdb=" O SER A 940 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG A 942 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 911 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE A 944 " --> pdb=" O ILE A 911 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL A 913 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 946 " --> pdb=" O VAL A 913 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 376 Processing sheet with id=AA5, first strand: chain 'B' and resid 393 through 394 Processing sheet with id=AA6, first strand: chain 'B' and resid 826 through 832 removed outlier: 6.530A pdb=" N THR B 790 " --> pdb=" O PHE B 826 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLN B 828 " --> pdb=" O THR B 790 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 792 " --> pdb=" O GLN B 828 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL B 830 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER B 794 " --> pdb=" O VAL B 830 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 832 " --> pdb=" O SER B 794 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE B 796 " --> pdb=" O ALA B 832 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 760 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 856 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA B 893 " --> pdb=" O VAL B 856 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET B 858 " --> pdb=" O ALA B 893 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B1135 " --> pdb=" O LYS B 894 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU B1136 " --> pdb=" O LYS B1102 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B1104 " --> pdb=" O LEU B1136 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B1138 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1106 " --> pdb=" O VAL B1138 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N GLU B 908 " --> pdb=" O ALA B1101 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU B1103 " --> pdb=" O GLU B 908 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 910 " --> pdb=" O LEU B1103 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU B1105 " --> pdb=" O ASN B 910 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 912 " --> pdb=" O LEU B1105 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN B1107 " --> pdb=" O ASP B 912 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B 907 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER B 940 " --> pdb=" O SER B 907 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY B 909 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG B 942 " --> pdb=" O GLY B 909 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE B 911 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE B 944 " --> pdb=" O ILE B 911 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 913 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 946 " --> pdb=" O VAL B 913 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1764 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: 4.31 Time building geometry restraints manager: 5.90 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: 4252 1.34 - 1.46: 3400 1.46 - 1.59: 6194 1.59 - 1.71: 0 1.71 - 1.83: 158 Bond restraints: 14004 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG B1201 " pdb=" O5 NAG B1201 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CA ARG A 548 " pdb=" C ARG A 548 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.64e+00 bond pdb=" CA ARG B 548 " pdb=" C ARG B 548 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.64e+00 bond pdb=" C HIS B 386 " pdb=" N ILE B 387 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.20e-02 6.94e+03 6.06e+00 ... (remaining 13999 not shown) Histogram of bond angle deviations from ideal: 96.42 - 103.94: 206 103.94 - 111.47: 6154 111.47 - 118.99: 5208 118.99 - 126.52: 7212 126.52 - 134.05: 234 Bond angle restraints: 19014 Sorted by residual: angle pdb=" C SER A 515 " pdb=" N ILE A 516 " pdb=" CA ILE A 516 " ideal model delta sigma weight residual 120.24 124.95 -4.71 6.30e-01 2.52e+00 5.58e+01 angle pdb=" C SER B 515 " pdb=" N ILE B 516 " pdb=" CA ILE B 516 " ideal model delta sigma weight residual 120.24 124.95 -4.71 6.30e-01 2.52e+00 5.58e+01 angle pdb=" N ARG A 593 " pdb=" CA ARG A 593 " pdb=" C ARG A 593 " ideal model delta sigma weight residual 111.36 117.64 -6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" N ARG B 593 " pdb=" CA ARG B 593 " pdb=" C ARG B 593 " ideal model delta sigma weight residual 111.36 117.58 -6.22 1.09e+00 8.42e-01 3.26e+01 angle pdb=" C ILE A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 19009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 7802 15.85 - 31.70: 402 31.70 - 47.54: 76 47.54 - 63.39: 8 63.39 - 79.24: 4 Dihedral angle restraints: 8292 sinusoidal: 3246 harmonic: 5046 Sorted by residual: dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 653 " pdb=" CB CYS A 653 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 271 " pdb=" SG CYS B 271 " pdb=" SG CYS B 653 " pdb=" CB CYS B 653 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CA SER A 471 " pdb=" C SER A 471 " pdb=" N LEU A 472 " pdb=" CA LEU A 472 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 8289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1596 0.054 - 0.108: 508 0.108 - 0.161: 94 0.161 - 0.215: 18 0.215 - 0.269: 4 Chirality restraints: 2220 Sorted by residual: chirality pdb=" C4 NAG B1201 " pdb=" C3 NAG B1201 " pdb=" C5 NAG B1201 " pdb=" O4 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C4 NAG A1201 " pdb=" C3 NAG A1201 " pdb=" C5 NAG A1201 " pdb=" O4 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG A 593 " pdb=" N ARG A 593 " pdb=" C ARG A 593 " pdb=" CB ARG A 593 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2217 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 643 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 644 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 643 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 644 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 826 " 0.016 2.00e-02 2.50e+03 1.56e-02 4.23e+00 pdb=" CG PHE B 826 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 826 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 826 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 826 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 826 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 826 " 0.002 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1210 2.73 - 3.27: 13751 3.27 - 3.81: 21977 3.81 - 4.36: 26266 4.36 - 4.90: 43243 Nonbonded interactions: 106447 Sorted by model distance: nonbonded pdb=" O LEU B 588 " pdb=" CD PRO B 592 " model vdw 2.186 3.440 nonbonded pdb=" O LEU A 588 " pdb=" CD PRO A 592 " model vdw 2.189 3.440 nonbonded pdb=" OG SER A 465 " pdb=" O6 NAG A1201 " model vdw 2.234 2.440 nonbonded pdb=" OG SER B 465 " pdb=" O6 NAG B1201 " model vdw 2.234 2.440 nonbonded pdb=" O ASP A 959 " pdb=" OG1 THR A 962 " model vdw 2.253 2.440 ... (remaining 106442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.590 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: 3.760 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 39.250 Find NCS groups from input model: 0.710 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 0.074 14004 Z= 0.447 Angle : 1.058 9.586 19014 Z= 0.608 Chirality : 0.055 0.269 2220 Planarity : 0.007 0.054 2358 Dihedral : 10.065 79.240 5034 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.15), residues: 1752 helix: -3.77 (0.10), residues: 870 sheet: -1.42 (0.44), residues: 126 loop : -2.94 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 406 HIS 0.012 0.003 HIS B 841 PHE 0.036 0.003 PHE B 826 TYR 0.014 0.003 TYR A 701 ARG 0.015 0.001 ARG A 968 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 386 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8631 (mm) cc_final: 0.8399 (tp) REVERT: A 314 MET cc_start: 0.8494 (tpt) cc_final: 0.8277 (tpt) REVERT: A 469 LEU cc_start: 0.7369 (tp) cc_final: 0.7041 (mp) REVERT: A 532 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 292 LEU cc_start: 0.8621 (mm) cc_final: 0.8387 (tp) REVERT: B 314 MET cc_start: 0.8483 (tpt) cc_final: 0.8264 (tpt) REVERT: B 469 LEU cc_start: 0.7362 (tp) cc_final: 0.7028 (mp) REVERT: B 532 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8025 (mt) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.2763 time to fit residues: 150.7516 Evaluate side-chains 215 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 0.0020 chunk 71 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 513 GLN A 596 GLN A 658 ASN A 680 HIS A 720 GLN A 751 HIS A 933 HIS A 966 HIS ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 513 GLN B 596 GLN B 658 ASN B 680 HIS B 720 GLN B 751 HIS B 933 HIS B 966 HIS ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14004 Z= 0.193 Angle : 0.671 9.099 19014 Z= 0.349 Chirality : 0.043 0.200 2220 Planarity : 0.005 0.037 2358 Dihedral : 6.301 55.813 1960 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.13 % Allowed : 11.36 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.17), residues: 1752 helix: -1.62 (0.14), residues: 974 sheet: -0.88 (0.41), residues: 146 loop : -2.95 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 406 HIS 0.010 0.001 HIS B 426 PHE 0.032 0.002 PHE A 538 TYR 0.014 0.002 TYR B 273 ARG 0.004 0.000 ARG B 990 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 261 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7975 (mt) REVERT: A 655 LEU cc_start: 0.9180 (tp) cc_final: 0.8888 (tp) REVERT: A 695 MET cc_start: 0.8282 (mtp) cc_final: 0.8031 (mtp) REVERT: A 712 MET cc_start: 0.7226 (ppp) cc_final: 0.6761 (ttt) REVERT: A 989 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7073 (mm-30) REVERT: B 532 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7977 (mt) REVERT: B 655 LEU cc_start: 0.9182 (tp) cc_final: 0.8889 (tp) REVERT: B 695 MET cc_start: 0.8283 (mtp) cc_final: 0.8035 (mtp) REVERT: B 712 MET cc_start: 0.7218 (ppp) cc_final: 0.6775 (ttt) REVERT: B 989 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7081 (mm-30) outliers start: 46 outliers final: 12 residues processed: 289 average time/residue: 0.2176 time to fit residues: 97.1427 Evaluate side-chains 225 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 HIS ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 14004 Z= 0.334 Angle : 0.730 10.184 19014 Z= 0.370 Chirality : 0.045 0.227 2220 Planarity : 0.004 0.032 2358 Dihedral : 6.184 53.187 1960 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 3.95 % Allowed : 13.88 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.18), residues: 1752 helix: -0.77 (0.16), residues: 956 sheet: -1.05 (0.41), residues: 140 loop : -2.68 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 914 HIS 0.006 0.002 HIS A 770 PHE 0.021 0.002 PHE A 538 TYR 0.018 0.002 TYR B 273 ARG 0.003 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 215 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.7235 (mmm) cc_final: 0.7028 (mmm) REVERT: A 532 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 655 LEU cc_start: 0.9201 (tp) cc_final: 0.8976 (tp) REVERT: A 695 MET cc_start: 0.8376 (mtp) cc_final: 0.8099 (mtp) REVERT: A 712 MET cc_start: 0.7313 (ppp) cc_final: 0.6977 (tmm) REVERT: A 1084 MET cc_start: 0.5775 (mmt) cc_final: 0.5144 (tpp) REVERT: B 532 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8009 (mp) REVERT: B 655 LEU cc_start: 0.9198 (tp) cc_final: 0.8975 (tp) REVERT: B 695 MET cc_start: 0.8375 (mtp) cc_final: 0.8115 (mtp) REVERT: B 712 MET cc_start: 0.7321 (ppp) cc_final: 0.6986 (tmm) REVERT: B 1084 MET cc_start: 0.5785 (mmt) cc_final: 0.5124 (tpp) outliers start: 58 outliers final: 31 residues processed: 257 average time/residue: 0.2162 time to fit residues: 87.8360 Evaluate side-chains 230 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 1135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 160 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14004 Z= 0.188 Angle : 0.631 10.221 19014 Z= 0.310 Chirality : 0.042 0.289 2220 Planarity : 0.003 0.030 2358 Dihedral : 5.600 45.608 1960 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.45 % Allowed : 15.65 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1752 helix: -0.07 (0.17), residues: 948 sheet: -0.76 (0.42), residues: 142 loop : -2.49 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 873 HIS 0.004 0.001 HIS A 918 PHE 0.021 0.001 PHE A 538 TYR 0.014 0.001 TYR B 965 ARG 0.002 0.000 ARG B 675 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7131 (tpt) cc_final: 0.6883 (tpt) REVERT: A 532 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8084 (mt) REVERT: A 655 LEU cc_start: 0.9032 (tp) cc_final: 0.8824 (tp) REVERT: A 712 MET cc_start: 0.7184 (ppp) cc_final: 0.6952 (tmm) REVERT: A 924 MET cc_start: 0.8267 (mmm) cc_final: 0.8009 (mpp) REVERT: A 1084 MET cc_start: 0.5678 (mmt) cc_final: 0.5220 (tpp) REVERT: B 189 MET cc_start: 0.7118 (tpt) cc_final: 0.6752 (tpt) REVERT: B 532 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8082 (mt) REVERT: B 655 LEU cc_start: 0.9030 (tp) cc_final: 0.8801 (tp) REVERT: B 712 MET cc_start: 0.7184 (ppp) cc_final: 0.6962 (tmm) REVERT: B 924 MET cc_start: 0.8267 (mmm) cc_final: 0.7996 (mpp) REVERT: B 1084 MET cc_start: 0.5695 (mmt) cc_final: 0.5184 (tpp) outliers start: 36 outliers final: 18 residues processed: 252 average time/residue: 0.2130 time to fit residues: 83.6798 Evaluate side-chains 232 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 873 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14004 Z= 0.281 Angle : 0.665 7.300 19014 Z= 0.335 Chirality : 0.043 0.241 2220 Planarity : 0.004 0.028 2358 Dihedral : 5.461 33.322 1960 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.24 % Allowed : 15.37 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1752 helix: 0.14 (0.17), residues: 948 sheet: -0.75 (0.43), residues: 142 loop : -2.47 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 914 HIS 0.007 0.002 HIS B 918 PHE 0.019 0.002 PHE B 963 TYR 0.015 0.002 TYR B 273 ARG 0.004 0.000 ARG B 990 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 209 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8195 (mt) REVERT: A 712 MET cc_start: 0.7355 (ppp) cc_final: 0.6934 (tmm) REVERT: A 1084 MET cc_start: 0.5635 (mmt) cc_final: 0.5225 (tpp) REVERT: B 532 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8165 (mt) REVERT: B 712 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6967 (tmm) REVERT: B 1084 MET cc_start: 0.5650 (mmt) cc_final: 0.5200 (tpp) outliers start: 77 outliers final: 44 residues processed: 257 average time/residue: 0.2206 time to fit residues: 88.0884 Evaluate side-chains 245 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 198 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 14004 Z= 0.252 Angle : 0.647 9.592 19014 Z= 0.321 Chirality : 0.043 0.267 2220 Planarity : 0.003 0.028 2358 Dihedral : 5.258 30.093 1960 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.83 % Allowed : 16.46 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 1752 helix: 0.27 (0.16), residues: 952 sheet: -0.67 (0.43), residues: 142 loop : -2.48 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 570 HIS 0.006 0.001 HIS B 918 PHE 0.019 0.001 PHE A 538 TYR 0.018 0.001 TYR A 965 ARG 0.002 0.000 ARG B 881 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 224 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8079 (mt) REVERT: A 712 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: A 1084 MET cc_start: 0.5377 (mmt) cc_final: 0.5101 (tpp) REVERT: B 532 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8074 (mt) REVERT: B 685 PHE cc_start: 0.7637 (t80) cc_final: 0.7432 (t80) REVERT: B 712 MET cc_start: 0.7357 (ppp) cc_final: 0.6976 (tmm) REVERT: B 1084 MET cc_start: 0.5405 (mmt) cc_final: 0.5099 (tpp) outliers start: 71 outliers final: 43 residues processed: 268 average time/residue: 0.2130 time to fit residues: 90.3665 Evaluate side-chains 246 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 200 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 902 ASN Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 169 optimal weight: 0.1980 chunk 106 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14004 Z= 0.182 Angle : 0.656 13.236 19014 Z= 0.313 Chirality : 0.043 0.275 2220 Planarity : 0.003 0.027 2358 Dihedral : 4.946 30.500 1960 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.40 % Allowed : 18.71 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1752 helix: 0.50 (0.17), residues: 952 sheet: -0.49 (0.46), residues: 140 loop : -2.37 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 873 HIS 0.005 0.001 HIS A 918 PHE 0.021 0.001 PHE B 650 TYR 0.010 0.001 TYR B 273 ARG 0.001 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8017 (mt) REVERT: A 712 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6878 (tmm) REVERT: B 532 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8043 (mt) REVERT: B 685 PHE cc_start: 0.7536 (t80) cc_final: 0.7302 (t80) REVERT: B 712 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6857 (tmm) REVERT: B 924 MET cc_start: 0.8182 (mmm) cc_final: 0.7921 (mpp) outliers start: 50 outliers final: 29 residues processed: 241 average time/residue: 0.1995 time to fit residues: 76.1520 Evaluate side-chains 233 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 chunk 154 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14004 Z= 0.247 Angle : 0.696 12.766 19014 Z= 0.339 Chirality : 0.044 0.291 2220 Planarity : 0.004 0.036 2358 Dihedral : 5.064 30.130 1960 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.29 % Allowed : 17.76 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1752 helix: 0.41 (0.16), residues: 954 sheet: -0.56 (0.45), residues: 140 loop : -2.42 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 570 HIS 0.004 0.001 HIS A 841 PHE 0.018 0.002 PHE B 650 TYR 0.011 0.001 TYR B 273 ARG 0.002 0.000 ARG A1113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 207 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8102 (mt) REVERT: A 712 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6913 (tmm) REVERT: A 924 MET cc_start: 0.8283 (mmm) cc_final: 0.7977 (mpp) REVERT: A 1108 MET cc_start: 0.7797 (ppp) cc_final: 0.7537 (ppp) REVERT: B 532 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 688 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7894 (tpp) REVERT: B 712 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6909 (tmm) REVERT: B 1108 MET cc_start: 0.7808 (ppp) cc_final: 0.7536 (ppp) outliers start: 63 outliers final: 49 residues processed: 248 average time/residue: 0.2103 time to fit residues: 81.9503 Evaluate side-chains 255 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 902 ASN Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 chunk 158 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 149 optimal weight: 0.1980 chunk 157 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 14004 Z= 0.225 Angle : 0.673 12.137 19014 Z= 0.326 Chirality : 0.044 0.305 2220 Planarity : 0.004 0.049 2358 Dihedral : 4.995 30.349 1960 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.22 % Allowed : 17.69 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1752 helix: 0.51 (0.17), residues: 956 sheet: -0.58 (0.45), residues: 140 loop : -2.33 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 873 HIS 0.003 0.001 HIS A 918 PHE 0.033 0.001 PHE A 963 TYR 0.010 0.001 TYR B 283 ARG 0.002 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.7021 (m-80) cc_final: 0.6663 (m-10) REVERT: A 532 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8047 (mt) REVERT: A 704 ILE cc_start: 0.8378 (mm) cc_final: 0.8031 (mm) REVERT: A 712 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6937 (tmm) REVERT: A 924 MET cc_start: 0.8224 (mmm) cc_final: 0.7939 (mpp) REVERT: A 1108 MET cc_start: 0.7779 (ppp) cc_final: 0.7517 (ppp) REVERT: B 451 TYR cc_start: 0.7010 (m-80) cc_final: 0.6666 (m-10) REVERT: B 532 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (mt) REVERT: B 688 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: B 712 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6893 (tmm) REVERT: B 1108 MET cc_start: 0.7804 (ppp) cc_final: 0.7539 (ppp) outliers start: 62 outliers final: 46 residues processed: 253 average time/residue: 0.2236 time to fit residues: 88.4987 Evaluate side-chains 254 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 902 ASN Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 14004 Z= 0.233 Angle : 0.687 12.316 19014 Z= 0.332 Chirality : 0.045 0.310 2220 Planarity : 0.004 0.058 2358 Dihedral : 4.955 30.223 1960 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.29 % Allowed : 18.16 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1752 helix: 0.52 (0.16), residues: 954 sheet: -0.63 (0.45), residues: 140 loop : -2.35 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 873 HIS 0.010 0.001 HIS A 841 PHE 0.024 0.001 PHE A 685 TYR 0.015 0.001 TYR B 283 ARG 0.002 0.000 ARG A1113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 213 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.7037 (m-80) cc_final: 0.6740 (m-10) REVERT: A 532 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8061 (mt) REVERT: A 704 ILE cc_start: 0.8426 (mm) cc_final: 0.8083 (mm) REVERT: A 712 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6863 (tmm) REVERT: A 924 MET cc_start: 0.8264 (mmm) cc_final: 0.7977 (mpp) REVERT: A 1108 MET cc_start: 0.7909 (ppp) cc_final: 0.7708 (ppp) REVERT: B 451 TYR cc_start: 0.7017 (m-80) cc_final: 0.6732 (m-10) REVERT: B 532 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8063 (mt) REVERT: B 688 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7723 (tpp) REVERT: B 704 ILE cc_start: 0.8262 (mm) cc_final: 0.7998 (mm) REVERT: B 712 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6859 (tmm) REVERT: B 1108 MET cc_start: 0.7940 (ppp) cc_final: 0.7731 (ppp) outliers start: 63 outliers final: 50 residues processed: 252 average time/residue: 0.2053 time to fit residues: 81.3481 Evaluate side-chains 254 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 199 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 902 ASN Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 HIS B 720 GLN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.098584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085549 restraints weight = 55953.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.087302 restraints weight = 32980.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.088514 restraints weight = 22783.000| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 14004 Z= 0.310 Angle : 0.755 13.002 19014 Z= 0.368 Chirality : 0.046 0.290 2220 Planarity : 0.004 0.062 2358 Dihedral : 5.292 30.000 1960 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.97 % Allowed : 18.03 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1752 helix: 0.27 (0.16), residues: 956 sheet: -0.78 (0.45), residues: 140 loop : -2.43 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 566 HIS 0.013 0.002 HIS A 841 PHE 0.066 0.002 PHE A 538 TYR 0.015 0.002 TYR B 273 ARG 0.002 0.000 ARG A1113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.75 seconds wall clock time: 50 minutes 3.41 seconds (3003.41 seconds total)