Starting phenix.real_space_refine on Fri Feb 16 00:20:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6que_4637/02_2024/6que_4637_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6que_4637/02_2024/6que_4637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6que_4637/02_2024/6que_4637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6que_4637/02_2024/6que_4637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6que_4637/02_2024/6que_4637_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6que_4637/02_2024/6que_4637_updated.pdb" } resolution = 3.7 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= 0.002 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 80 5.16 5 C 8822 2.51 5 N 2283 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13791 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7620 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain: "B" Number of atoms: 6035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6035 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 39, 'TRANS': 787} Chain breaks: 1 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'NAD': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.07, per 1000 atoms: 0.59 Number of scatterers: 13791 At special positions: 0 Unit cell: (140.58, 130.995, 132.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 7 15.00 O 2599 8.00 N 2283 7.00 C 8822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.7 seconds 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 6 sheets defined 51.4% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.576A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.713A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.545A pdb=" N GLU A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.038A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.574A pdb=" N ALA A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 448 removed outlier: 3.969A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 474 removed outlier: 3.790A pdb=" N TRP A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 501 removed outlier: 4.141A pdb=" N HIS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER A 482 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Proline residue: A 483 - end of helix removed outlier: 3.981A pdb=" N SER A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 495 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 500 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 501 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.731A pdb=" N ALA A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 571 Proline residue: A 558 - end of helix removed outlier: 4.335A pdb=" N VAL A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 564 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A 568 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 571 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.757A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 623 removed outlier: 4.093A pdb=" N GLY A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 648 Processing helix chain 'A' and resid 656 through 681 removed outlier: 3.914A pdb=" N SER A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 667 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 691 through 721 removed outlier: 3.775A pdb=" N THR A 695 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 696 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 698 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY A 702 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 706 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE A 710 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 711 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 712 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS A 719 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 721 " --> pdb=" O GLY A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 747 Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 787 through 809 removed outlier: 4.214A pdb=" N VAL A 794 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 799 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 802 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 836 removed outlier: 3.550A pdb=" N SER A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 898 through 910 removed outlier: 3.728A pdb=" N ASP A 903 " --> pdb=" O TYR A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 937 Processing helix chain 'A' and resid 941 through 943 No H-bonds generated for 'chain 'A' and resid 941 through 943' Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1026 through 1041 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 60 through 66 Processing helix chain 'B' and resid 98 through 101 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 251 through 266 removed outlier: 4.240A pdb=" N LYS B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 4.491A pdb=" N SER B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 334 through 356 removed outlier: 4.015A pdb=" N ALA B 338 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR B 339 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 341 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER B 342 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR B 345 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 350 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 351 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 354 " --> pdb=" O LYS B 351 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE B 356 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 426 through 448 Processing helix chain 'B' and resid 453 through 470 Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.768A pdb=" N SER B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 512 through 542 removed outlier: 3.700A pdb=" N SER B 525 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE B 542 " --> pdb=" O MET B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 562 Proline residue: B 558 - end of helix Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.801A pdb=" N ALA B 568 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 596 removed outlier: 4.180A pdb=" N SER B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 621 Processing helix chain 'B' and resid 627 through 649 removed outlier: 3.560A pdb=" N ALA B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 681 removed outlier: 3.600A pdb=" N VAL B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA B 661 " --> pdb=" O PRO B 657 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 667 " --> pdb=" O PHE B 663 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 668 " --> pdb=" O HIS B 664 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 720 removed outlier: 4.895A pdb=" N ALA B 699 " --> pdb=" O THR B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 746 Processing helix chain 'B' and resid 750 through 752 No H-bonds generated for 'chain 'B' and resid 750 through 752' Processing helix chain 'B' and resid 758 through 781 Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.827A pdb=" N THR B 793 " --> pdb=" O PRO B 789 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 836 Processing helix chain 'B' and resid 842 through 845 No H-bonds generated for 'chain 'B' and resid 842 through 845' Processing sheet with id= A, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.469A pdb=" N ASN A 45 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 18 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A 47 " --> pdb=" O VAL A 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.902A pdb=" N THR A 130 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N SER A 110 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 132 " --> pdb=" O SER A 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 187 through 190 removed outlier: 6.415A pdb=" N ILE A 270 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL A 190 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 272 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 299 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER A 273 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 301 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N THR A 326 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP A 302 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 328 " --> pdb=" O ASP A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 914 through 917 removed outlier: 6.407A pdb=" N LEU A 959 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR A 887 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 961 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLN A 994 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL A 962 " --> pdb=" O GLN A 994 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 996 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 130 through 133 removed outlier: 3.864A pdb=" N SER B 110 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN B 45 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 18 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 47 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLN B 69 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.285A pdb=" N ILE B 270 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL B 190 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 272 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B 299 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N SER B 273 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 301 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR B 326 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASP B 302 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 328 " --> pdb=" O ASP B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 611 hydrogen bonds defined for protein. 1605 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: 4.57 Time building geometry restraints manager: 6.02 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: 4230 1.34 - 1.46: 2730 1.46 - 1.58: 6938 1.58 - 1.70: 13 1.70 - 1.82: 142 Bond restraints: 14053 Sorted by residual: bond pdb=" O2B NAP A1101 " pdb=" P2B NAP A1101 " ideal model delta sigma weight residual 1.736 1.580 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" O3 NAD A1102 " pdb=" PA NAD A1102 " ideal model delta sigma weight residual 1.653 1.589 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 NAD B1101 " pdb=" PA NAD B1101 " ideal model delta sigma weight residual 1.653 1.589 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C THR B 546 " pdb=" N ASP B 547 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.00e+01 bond pdb=" O5D NAP A1101 " pdb=" PN NAP A1101 " ideal model delta sigma weight residual 1.649 1.590 0.059 2.00e-02 2.50e+03 8.72e+00 ... (remaining 14048 not shown) Histogram of bond angle deviations from ideal: 95.00 - 102.87: 110 102.87 - 110.74: 4787 110.74 - 118.62: 6568 118.62 - 126.49: 7478 126.49 - 134.36: 167 Bond angle restraints: 19110 Sorted by residual: angle pdb=" N ALA A 518 " pdb=" CA ALA A 518 " pdb=" C ALA A 518 " ideal model delta sigma weight residual 113.18 103.98 9.20 1.33e+00 5.65e-01 4.78e+01 angle pdb=" C GLN B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 122.46 131.85 -9.39 1.41e+00 5.03e-01 4.43e+01 angle pdb=" C PHE B 371 " pdb=" N ASP B 372 " pdb=" CA ASP B 372 " ideal model delta sigma weight residual 122.44 114.57 7.87 1.19e+00 7.06e-01 4.38e+01 angle pdb=" C ALA A 38 " pdb=" N LEU A 39 " pdb=" CA LEU A 39 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C ALA B 38 " pdb=" N LEU B 39 " pdb=" CA LEU B 39 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 ... (remaining 19105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 7937 16.23 - 32.46: 382 32.46 - 48.69: 87 48.69 - 64.92: 35 64.92 - 81.16: 23 Dihedral angle restraints: 8464 sinusoidal: 3233 harmonic: 5231 Sorted by residual: dihedral pdb=" CA LYS B 399 " pdb=" C LYS B 399 " pdb=" N ASN B 400 " pdb=" CA ASN B 400 " ideal model delta harmonic sigma weight residual -180.00 -138.96 -41.04 0 5.00e+00 4.00e-02 6.74e+01 dihedral pdb=" CA THR B 424 " pdb=" C THR B 424 " pdb=" N PRO B 425 " pdb=" CA PRO B 425 " ideal model delta harmonic sigma weight residual 180.00 -149.47 -30.53 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA GLN A 37 " pdb=" C GLN A 37 " pdb=" N ALA A 38 " pdb=" CA ALA A 38 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 8461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1647 0.059 - 0.119: 507 0.119 - 0.178: 102 0.178 - 0.238: 16 0.238 - 0.297: 3 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA TRP B 474 " pdb=" N TRP B 474 " pdb=" C TRP B 474 " pdb=" CB TRP B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA PHE B 365 " pdb=" N PHE B 365 " pdb=" C PHE B 365 " pdb=" CB PHE B 365 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PHE B 752 " pdb=" N PHE B 752 " pdb=" C PHE B 752 " pdb=" CB PHE B 752 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2272 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 18 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 19 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 19 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 19 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 752 " -0.025 2.00e-02 2.50e+03 2.19e-02 8.38e+00 pdb=" CG PHE B 752 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 752 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 752 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 752 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 752 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 752 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 673 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C LEU B 673 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 673 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 674 " -0.017 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2725 2.76 - 3.30: 13405 3.30 - 3.83: 22833 3.83 - 4.37: 26325 4.37 - 4.90: 44592 Nonbonded interactions: 109880 Sorted by model distance: nonbonded pdb=" O TYR B 566 " pdb=" OG SER B 569 " model vdw 2.230 2.440 nonbonded pdb=" O GLN B 340 " pdb=" OG1 THR B 343 " model vdw 2.267 2.440 nonbonded pdb=" O PHE A 954 " pdb=" OG SER A 992 " model vdw 2.275 2.440 nonbonded pdb=" O MET B 485 " pdb=" OG1 THR B 488 " model vdw 2.285 2.440 nonbonded pdb=" O GLY A 776 " pdb=" OG1 THR A 780 " model vdw 2.287 2.440 ... (remaining 109875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.080 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: 1.320 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 40.320 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.009 0.156 14053 Z= 0.572 Angle : 1.104 11.811 19110 Z= 0.599 Chirality : 0.059 0.297 2275 Planarity : 0.008 0.073 2416 Dihedral : 12.099 81.155 5156 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.36 % Rotamer: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.06 % 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: -3.49 (0.16), residues: 1859 helix: -1.83 (0.13), residues: 985 sheet: -1.62 (0.41), residues: 147 loop : -3.04 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 474 HIS 0.011 0.003 HIS A 664 PHE 0.051 0.004 PHE B 752 TYR 0.027 0.003 TYR B 330 ARG 0.008 0.001 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 333 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8585 (tp30) cc_final: 0.8272 (tm-30) REVERT: A 60 ASP cc_start: 0.9161 (m-30) cc_final: 0.8822 (t70) REVERT: A 77 LEU cc_start: 0.9391 (mt) cc_final: 0.9079 (tp) REVERT: A 172 PHE cc_start: 0.9237 (m-10) cc_final: 0.8879 (m-10) REVERT: A 249 MET cc_start: 0.7611 (mmp) cc_final: 0.7355 (mmm) REVERT: A 286 PHE cc_start: 0.8659 (m-80) cc_final: 0.8230 (m-10) REVERT: A 288 LYS cc_start: 0.9299 (ptmm) cc_final: 0.9052 (ptpt) REVERT: A 296 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6704 (tm-30) REVERT: A 337 MET cc_start: 0.8594 (mtp) cc_final: 0.8386 (mtp) REVERT: A 345 TYR cc_start: 0.9065 (t80) cc_final: 0.8861 (t80) REVERT: A 414 GLU cc_start: 0.8046 (tt0) cc_final: 0.7824 (mt-10) REVERT: A 430 MET cc_start: 0.8947 (tpt) cc_final: 0.8674 (tpt) REVERT: A 458 MET cc_start: 0.9234 (tpp) cc_final: 0.8981 (tpp) REVERT: A 507 LEU cc_start: 0.8938 (mm) cc_final: 0.8694 (tt) REVERT: A 754 MET cc_start: 0.7578 (mpt) cc_final: 0.7048 (mmp) REVERT: A 764 CYS cc_start: 0.8918 (m) cc_final: 0.8631 (t) REVERT: A 869 ILE cc_start: 0.8925 (pt) cc_final: 0.8546 (pt) REVERT: A 873 ASN cc_start: 0.8463 (m110) cc_final: 0.7916 (t0) REVERT: A 877 MET cc_start: 0.9124 (ttp) cc_final: 0.8761 (ptm) REVERT: A 903 ASP cc_start: 0.8636 (t70) cc_final: 0.8237 (t0) REVERT: A 907 MET cc_start: 0.8713 (mtt) cc_final: 0.8294 (mmm) REVERT: A 947 MET cc_start: 0.9091 (ttp) cc_final: 0.8645 (tmm) REVERT: A 1021 MET cc_start: 0.8833 (mmm) cc_final: 0.8504 (mmm) REVERT: B 109 ILE cc_start: 0.8759 (mm) cc_final: 0.8323 (mm) REVERT: B 286 PHE cc_start: 0.8791 (m-80) cc_final: 0.8521 (m-80) REVERT: B 366 GLU cc_start: 0.8606 (tt0) cc_final: 0.8382 (tm-30) REVERT: B 458 MET cc_start: 0.8999 (tpp) cc_final: 0.8446 (tpp) REVERT: B 477 THR cc_start: 0.9384 (m) cc_final: 0.9174 (p) REVERT: B 538 MET cc_start: 0.8887 (mtp) cc_final: 0.8592 (mtp) REVERT: B 663 PHE cc_start: 0.8920 (m-10) cc_final: 0.8693 (m-10) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.2473 time to fit residues: 125.3799 Evaluate side-chains 182 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 8.9990 chunk 140 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 838 ASN A 873 ASN A 931 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 340 GLN B 348 ASN B 489 ASN B 527 ASN B 735 HIS B 796 ASN B 813 ASN B 838 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14053 Z= 0.318 Angle : 0.705 11.507 19110 Z= 0.355 Chirality : 0.044 0.218 2275 Planarity : 0.005 0.049 2416 Dihedral : 8.855 51.343 2139 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 3.56 % Allowed : 11.03 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.66 (0.19), residues: 1859 helix: 0.06 (0.16), residues: 990 sheet: -1.32 (0.44), residues: 149 loop : -2.74 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 801 HIS 0.006 0.001 HIS A 664 PHE 0.035 0.002 PHE B 365 TYR 0.015 0.002 TYR B 330 ARG 0.004 0.001 ARG A 925 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.9151 (m-30) cc_final: 0.8839 (t0) REVERT: A 258 MET cc_start: 0.9254 (ttm) cc_final: 0.8952 (tmm) REVERT: A 288 LYS cc_start: 0.9313 (ptmm) cc_final: 0.8942 (ptpp) REVERT: A 296 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6628 (tm-30) REVERT: A 337 MET cc_start: 0.8643 (mtp) cc_final: 0.8381 (mtp) REVERT: A 430 MET cc_start: 0.8912 (tpt) cc_final: 0.8550 (tpt) REVERT: A 754 MET cc_start: 0.7410 (mpt) cc_final: 0.6760 (mmp) REVERT: A 838 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 877 MET cc_start: 0.9030 (ttp) cc_final: 0.8665 (ptm) REVERT: A 903 ASP cc_start: 0.8679 (t70) cc_final: 0.8094 (t0) REVERT: A 947 MET cc_start: 0.9136 (ttp) cc_final: 0.8638 (tmm) REVERT: A 1019 THR cc_start: 0.8815 (m) cc_final: 0.8392 (t) REVERT: B 286 PHE cc_start: 0.8914 (m-80) cc_final: 0.8484 (m-80) REVERT: B 290 MET cc_start: 0.8884 (mtp) cc_final: 0.8648 (mtm) REVERT: B 337 MET cc_start: 0.9146 (mtp) cc_final: 0.8456 (mtp) REVERT: B 458 MET cc_start: 0.8956 (tpp) cc_final: 0.8710 (tpp) REVERT: B 477 THR cc_start: 0.9423 (m) cc_final: 0.9199 (p) REVERT: B 829 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8219 (tt) outliers start: 51 outliers final: 27 residues processed: 233 average time/residue: 0.1996 time to fit residues: 74.3865 Evaluate side-chains 179 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 838 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 139 optimal weight: 0.1980 chunk 114 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 24 GLN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14053 Z= 0.255 Angle : 0.657 10.348 19110 Z= 0.326 Chirality : 0.043 0.239 2275 Planarity : 0.005 0.050 2416 Dihedral : 7.752 55.949 2139 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 3.77 % Allowed : 13.27 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.94 (0.20), residues: 1859 helix: 0.75 (0.17), residues: 979 sheet: -0.87 (0.49), residues: 140 loop : -2.54 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 801 HIS 0.005 0.001 HIS A 664 PHE 0.029 0.002 PHE A 365 TYR 0.016 0.001 TYR A 704 ARG 0.003 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 170 time to evaluate : 1.636 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.9093 (m-30) cc_final: 0.8753 (t0) REVERT: A 258 MET cc_start: 0.9226 (ttm) cc_final: 0.8957 (tmm) REVERT: A 288 LYS cc_start: 0.9334 (ptmm) cc_final: 0.8980 (ptpp) REVERT: A 296 GLU cc_start: 0.7611 (mm-30) cc_final: 0.6565 (tm-30) REVERT: A 430 MET cc_start: 0.8777 (tpt) cc_final: 0.8457 (tpt) REVERT: A 754 MET cc_start: 0.7408 (mpt) cc_final: 0.6699 (mmp) REVERT: A 877 MET cc_start: 0.9017 (ttp) cc_final: 0.8670 (ptm) REVERT: A 903 ASP cc_start: 0.8442 (t70) cc_final: 0.8115 (t0) REVERT: A 947 MET cc_start: 0.9169 (ttp) cc_final: 0.8646 (tmm) REVERT: A 997 VAL cc_start: 0.8848 (t) cc_final: 0.8304 (p) REVERT: A 1019 THR cc_start: 0.8793 (m) cc_final: 0.8438 (t) REVERT: B 286 PHE cc_start: 0.8912 (m-80) cc_final: 0.8448 (m-80) REVERT: B 290 MET cc_start: 0.8847 (mtp) cc_final: 0.8572 (mtm) REVERT: B 337 MET cc_start: 0.9193 (mtp) cc_final: 0.8533 (mtp) REVERT: B 345 TYR cc_start: 0.9224 (t80) cc_final: 0.8978 (t80) REVERT: B 458 MET cc_start: 0.8933 (tpp) cc_final: 0.8616 (tpp) REVERT: B 477 THR cc_start: 0.9451 (m) cc_final: 0.9215 (p) REVERT: B 592 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8498 (mm) REVERT: B 742 LEU cc_start: 0.8482 (mt) cc_final: 0.8191 (mt) REVERT: B 775 MET cc_start: 0.8658 (tpp) cc_final: 0.8026 (tpt) REVERT: B 829 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8191 (tt) outliers start: 54 outliers final: 37 residues processed: 213 average time/residue: 0.1975 time to fit residues: 68.3312 Evaluate side-chains 189 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 0.0570 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14053 Z= 0.206 Angle : 0.617 9.084 19110 Z= 0.302 Chirality : 0.042 0.249 2275 Planarity : 0.004 0.043 2416 Dihedral : 7.211 58.426 2139 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 4.40 % Allowed : 13.90 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.47 (0.20), residues: 1859 helix: 1.16 (0.17), residues: 976 sheet: -0.76 (0.49), residues: 140 loop : -2.32 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 801 HIS 0.005 0.001 HIS A 664 PHE 0.026 0.002 PHE A 365 TYR 0.019 0.001 TYR B 551 ARG 0.002 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.9042 (m-30) cc_final: 0.8779 (t0) REVERT: A 258 MET cc_start: 0.9202 (ttm) cc_final: 0.8939 (tmm) REVERT: A 288 LYS cc_start: 0.9338 (ptmm) cc_final: 0.8988 (ptpp) REVERT: A 296 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6602 (tm-30) REVERT: A 376 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8938 (tpt) REVERT: A 430 MET cc_start: 0.8745 (tpt) cc_final: 0.8391 (tpt) REVERT: A 754 MET cc_start: 0.7329 (mpt) cc_final: 0.6644 (mmp) REVERT: A 877 MET cc_start: 0.9002 (ttp) cc_final: 0.8694 (ptm) REVERT: A 903 ASP cc_start: 0.8448 (t70) cc_final: 0.8139 (t0) REVERT: A 947 MET cc_start: 0.9158 (ttp) cc_final: 0.8622 (tmm) REVERT: A 1019 THR cc_start: 0.8748 (m) cc_final: 0.8423 (t) REVERT: B 274 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.8987 (p) REVERT: B 286 PHE cc_start: 0.8890 (m-80) cc_final: 0.8431 (m-80) REVERT: B 290 MET cc_start: 0.8833 (mtp) cc_final: 0.8586 (mtm) REVERT: B 337 MET cc_start: 0.9198 (mtp) cc_final: 0.8567 (mtp) REVERT: B 458 MET cc_start: 0.8946 (tpp) cc_final: 0.8589 (tpp) REVERT: B 477 THR cc_start: 0.9445 (m) cc_final: 0.9229 (p) REVERT: B 592 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8477 (mm) REVERT: B 742 LEU cc_start: 0.8388 (mt) cc_final: 0.8040 (mt) REVERT: B 775 MET cc_start: 0.8608 (tpp) cc_final: 0.8021 (tpt) outliers start: 63 outliers final: 38 residues processed: 219 average time/residue: 0.2017 time to fit residues: 71.6342 Evaluate side-chains 194 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.4980 chunk 101 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 ASN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14053 Z= 0.223 Angle : 0.616 10.010 19110 Z= 0.301 Chirality : 0.042 0.236 2275 Planarity : 0.004 0.042 2416 Dihedral : 6.891 55.264 2139 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.83 % Favored : 93.11 % Rotamer: Outliers : 4.54 % Allowed : 14.73 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.22 (0.21), residues: 1859 helix: 1.34 (0.17), residues: 983 sheet: -0.60 (0.50), residues: 140 loop : -2.20 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 801 HIS 0.005 0.001 HIS A 664 PHE 0.023 0.002 PHE A 393 TYR 0.014 0.001 TYR B 551 ARG 0.002 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 170 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 97 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.7697 (t70) REVERT: A 258 MET cc_start: 0.9187 (ttm) cc_final: 0.8930 (tmm) REVERT: A 288 LYS cc_start: 0.9349 (ptmm) cc_final: 0.8995 (ptpp) REVERT: A 296 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6537 (tm-30) REVERT: A 337 MET cc_start: 0.8885 (mmm) cc_final: 0.8535 (mmm) REVERT: A 430 MET cc_start: 0.8769 (tpt) cc_final: 0.8374 (tpt) REVERT: A 754 MET cc_start: 0.7400 (mpt) cc_final: 0.6630 (mmp) REVERT: A 877 MET cc_start: 0.8951 (ttp) cc_final: 0.8674 (ptm) REVERT: A 903 ASP cc_start: 0.8443 (t70) cc_final: 0.8148 (t0) REVERT: A 947 MET cc_start: 0.9142 (ttp) cc_final: 0.8620 (tmm) REVERT: A 1019 THR cc_start: 0.8728 (m) cc_final: 0.8390 (t) REVERT: B 274 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.8985 (p) REVERT: B 286 PHE cc_start: 0.8894 (m-80) cc_final: 0.8385 (m-80) REVERT: B 337 MET cc_start: 0.9215 (mtp) cc_final: 0.9014 (mtp) REVERT: B 458 MET cc_start: 0.8989 (tpp) cc_final: 0.8620 (tpp) REVERT: B 538 MET cc_start: 0.8783 (ttp) cc_final: 0.8560 (ttp) REVERT: B 592 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8514 (mm) REVERT: B 742 LEU cc_start: 0.8398 (mt) cc_final: 0.8068 (mt) REVERT: B 775 MET cc_start: 0.8594 (tpp) cc_final: 0.8130 (tpp) REVERT: B 829 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 65 outliers final: 44 residues processed: 221 average time/residue: 0.2166 time to fit residues: 78.6546 Evaluate side-chains 200 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 152 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 44 optimal weight: 0.0370 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14053 Z= 0.211 Angle : 0.615 9.373 19110 Z= 0.300 Chirality : 0.042 0.263 2275 Planarity : 0.004 0.039 2416 Dihedral : 6.685 54.076 2139 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.83 % Favored : 93.11 % Rotamer: Outliers : 4.26 % Allowed : 15.71 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.05 (0.21), residues: 1859 helix: 1.47 (0.17), residues: 982 sheet: -0.41 (0.50), residues: 132 loop : -2.12 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 801 HIS 0.011 0.001 HIS A 97 PHE 0.022 0.001 PHE B 365 TYR 0.013 0.001 TYR A 683 ARG 0.002 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 164 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.9199 (ttm) cc_final: 0.8937 (tmm) REVERT: A 288 LYS cc_start: 0.9343 (ptmm) cc_final: 0.8994 (ptpp) REVERT: A 296 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6543 (tm-30) REVERT: A 337 MET cc_start: 0.8850 (mmm) cc_final: 0.8500 (mmm) REVERT: A 376 MET cc_start: 0.9089 (mmp) cc_final: 0.8868 (mmm) REVERT: A 430 MET cc_start: 0.8758 (tpt) cc_final: 0.8363 (tpt) REVERT: A 754 MET cc_start: 0.7070 (mpt) cc_final: 0.6306 (mmp) REVERT: A 877 MET cc_start: 0.8901 (ttp) cc_final: 0.8700 (ptm) REVERT: A 903 ASP cc_start: 0.8397 (t70) cc_final: 0.8149 (t0) REVERT: A 984 MET cc_start: 0.8277 (tpp) cc_final: 0.7867 (tpp) REVERT: A 1019 THR cc_start: 0.8705 (m) cc_final: 0.8379 (t) REVERT: B 63 TYR cc_start: 0.9109 (m-80) cc_final: 0.8813 (m-10) REVERT: B 274 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.8984 (p) REVERT: B 286 PHE cc_start: 0.9007 (m-80) cc_final: 0.8519 (m-80) REVERT: B 337 MET cc_start: 0.9192 (mtp) cc_final: 0.8955 (mtp) REVERT: B 458 MET cc_start: 0.8992 (tpp) cc_final: 0.8622 (tpp) REVERT: B 538 MET cc_start: 0.8767 (ttp) cc_final: 0.8501 (ttp) REVERT: B 592 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 742 LEU cc_start: 0.8414 (mt) cc_final: 0.8066 (mt) REVERT: B 775 MET cc_start: 0.8565 (tpp) cc_final: 0.7967 (tpt) REVERT: B 829 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8160 (tt) outliers start: 61 outliers final: 45 residues processed: 212 average time/residue: 0.1856 time to fit residues: 64.4141 Evaluate side-chains 206 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN B 378 HIS B 481 HIS B 527 ASN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14053 Z= 0.263 Angle : 0.649 10.626 19110 Z= 0.315 Chirality : 0.044 0.345 2275 Planarity : 0.004 0.038 2416 Dihedral : 6.648 53.234 2139 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.53 % Favored : 92.42 % Rotamer: Outliers : 4.40 % Allowed : 15.99 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.04 (0.21), residues: 1859 helix: 1.45 (0.17), residues: 984 sheet: -0.52 (0.50), residues: 133 loop : -2.04 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 474 HIS 0.010 0.001 HIS B 378 PHE 0.025 0.001 PHE A 393 TYR 0.014 0.001 TYR B 551 ARG 0.003 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 162 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7750 (ptp-110) REVERT: A 258 MET cc_start: 0.9214 (ttm) cc_final: 0.8943 (tmm) REVERT: A 288 LYS cc_start: 0.9373 (ptmm) cc_final: 0.9025 (ptpp) REVERT: A 296 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6506 (tm-30) REVERT: A 319 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 337 MET cc_start: 0.8942 (mmm) cc_final: 0.8494 (mmm) REVERT: A 376 MET cc_start: 0.9139 (mmp) cc_final: 0.8915 (mmm) REVERT: A 430 MET cc_start: 0.8798 (tpt) cc_final: 0.8411 (tpt) REVERT: A 754 MET cc_start: 0.6897 (mpt) cc_final: 0.6229 (mmp) REVERT: A 877 MET cc_start: 0.8901 (ttp) cc_final: 0.8656 (ptm) REVERT: A 903 ASP cc_start: 0.8407 (t70) cc_final: 0.8193 (t0) REVERT: A 984 MET cc_start: 0.8359 (tpp) cc_final: 0.7990 (tpp) REVERT: A 1019 THR cc_start: 0.8709 (m) cc_final: 0.8399 (t) REVERT: B 274 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.8994 (p) REVERT: B 286 PHE cc_start: 0.9069 (m-80) cc_final: 0.8701 (m-80) REVERT: B 337 MET cc_start: 0.9234 (mtp) cc_final: 0.8963 (mtp) REVERT: B 386 MET cc_start: 0.7797 (tmm) cc_final: 0.7570 (tmm) REVERT: B 458 MET cc_start: 0.8998 (tpp) cc_final: 0.8681 (tpp) REVERT: B 474 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.8109 (m100) REVERT: B 538 MET cc_start: 0.8783 (ttp) cc_final: 0.8525 (ttp) REVERT: B 592 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8519 (mm) REVERT: B 737 LEU cc_start: 0.8199 (tp) cc_final: 0.7993 (tp) REVERT: B 742 LEU cc_start: 0.8480 (mt) cc_final: 0.8202 (mt) REVERT: B 775 MET cc_start: 0.8653 (tpp) cc_final: 0.8116 (tpt) REVERT: B 829 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8150 (tt) outliers start: 63 outliers final: 44 residues processed: 212 average time/residue: 0.2013 time to fit residues: 68.8578 Evaluate side-chains 200 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 474 TRP Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 0.0000 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS B 481 HIS B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14053 Z= 0.189 Angle : 0.619 10.018 19110 Z= 0.299 Chirality : 0.043 0.368 2275 Planarity : 0.004 0.036 2416 Dihedral : 6.451 53.547 2139 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % Rotamer: Outliers : 3.84 % Allowed : 17.46 % Favored : 78.70 % 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: 0.11 (0.21), residues: 1859 helix: 1.57 (0.17), residues: 985 sheet: -0.26 (0.50), residues: 130 loop : -2.03 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 474 HIS 0.004 0.001 HIS A 664 PHE 0.028 0.001 PHE A 365 TYR 0.012 0.001 TYR A 683 ARG 0.002 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 170 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7760 (ptp-110) REVERT: A 258 MET cc_start: 0.9195 (ttm) cc_final: 0.8933 (tmm) REVERT: A 288 LYS cc_start: 0.9354 (ptmm) cc_final: 0.8989 (ptpp) REVERT: A 296 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6637 (tm-30) REVERT: A 319 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7465 (tp) REVERT: A 337 MET cc_start: 0.8918 (mmm) cc_final: 0.8462 (mmm) REVERT: A 376 MET cc_start: 0.9139 (mmp) cc_final: 0.8919 (mmm) REVERT: A 430 MET cc_start: 0.8757 (tpt) cc_final: 0.8361 (tpt) REVERT: A 580 MET cc_start: 0.8988 (tpt) cc_final: 0.8765 (tpt) REVERT: A 754 MET cc_start: 0.6889 (mpt) cc_final: 0.6198 (mmp) REVERT: A 984 MET cc_start: 0.8336 (tpp) cc_final: 0.8115 (tpp) REVERT: A 1019 THR cc_start: 0.8668 (m) cc_final: 0.8361 (t) REVERT: B 63 TYR cc_start: 0.9077 (m-80) cc_final: 0.8784 (m-10) REVERT: B 274 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 290 MET cc_start: 0.8470 (ptm) cc_final: 0.8256 (ptm) REVERT: B 337 MET cc_start: 0.9188 (mtp) cc_final: 0.8933 (mtp) REVERT: B 458 MET cc_start: 0.8996 (tpp) cc_final: 0.8580 (tpp) REVERT: B 474 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.8118 (m100) REVERT: B 538 MET cc_start: 0.8629 (ttp) cc_final: 0.8383 (ttp) REVERT: B 592 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 737 LEU cc_start: 0.8210 (tp) cc_final: 0.7994 (tp) REVERT: B 742 LEU cc_start: 0.8413 (mt) cc_final: 0.8141 (mt) REVERT: B 775 MET cc_start: 0.8556 (tpp) cc_final: 0.8040 (tpt) REVERT: B 829 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8190 (tt) outliers start: 55 outliers final: 40 residues processed: 210 average time/residue: 0.1969 time to fit residues: 67.0301 Evaluate side-chains 201 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 156 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 474 TRP Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 72 optimal weight: 0.0980 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 50.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 HIS B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14053 Z= 0.203 Angle : 0.630 10.389 19110 Z= 0.304 Chirality : 0.043 0.379 2275 Planarity : 0.004 0.034 2416 Dihedral : 6.355 54.822 2139 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 3.70 % Allowed : 18.58 % Favored : 77.72 % 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: 0.19 (0.21), residues: 1859 helix: 1.62 (0.17), residues: 988 sheet: -0.30 (0.50), residues: 130 loop : -1.96 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 474 HIS 0.004 0.001 HIS A 664 PHE 0.028 0.001 PHE A 365 TYR 0.013 0.001 TYR A 683 ARG 0.002 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 164 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7712 (ptp-110) REVERT: A 172 PHE cc_start: 0.9274 (m-80) cc_final: 0.9021 (t80) REVERT: A 258 MET cc_start: 0.9185 (ttm) cc_final: 0.8949 (tmm) REVERT: A 288 LYS cc_start: 0.9343 (ptmm) cc_final: 0.8983 (ptpp) REVERT: A 296 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6683 (tm-30) REVERT: A 319 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 337 MET cc_start: 0.8937 (mmm) cc_final: 0.8453 (mmm) REVERT: A 376 MET cc_start: 0.9148 (mmp) cc_final: 0.8933 (mmm) REVERT: A 430 MET cc_start: 0.8692 (tpt) cc_final: 0.8035 (ptm) REVERT: A 754 MET cc_start: 0.6842 (mpt) cc_final: 0.6153 (mmp) REVERT: A 903 ASP cc_start: 0.8476 (t0) cc_final: 0.8264 (t0) REVERT: A 984 MET cc_start: 0.8327 (tpp) cc_final: 0.7896 (tpp) REVERT: A 1019 THR cc_start: 0.8651 (m) cc_final: 0.8358 (t) REVERT: B 274 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.8999 (p) REVERT: B 290 MET cc_start: 0.8517 (ptm) cc_final: 0.8282 (ptm) REVERT: B 337 MET cc_start: 0.9201 (mtp) cc_final: 0.8920 (mtp) REVERT: B 458 MET cc_start: 0.9021 (tpp) cc_final: 0.8561 (tpp) REVERT: B 503 MET cc_start: 0.7275 (mtm) cc_final: 0.6382 (ptp) REVERT: B 538 MET cc_start: 0.8613 (ttp) cc_final: 0.8356 (ttp) REVERT: B 592 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 742 LEU cc_start: 0.8373 (mt) cc_final: 0.8123 (mt) REVERT: B 775 MET cc_start: 0.8547 (tpp) cc_final: 0.8031 (tpt) REVERT: B 829 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8197 (tt) outliers start: 53 outliers final: 40 residues processed: 204 average time/residue: 0.2094 time to fit residues: 69.8214 Evaluate side-chains 204 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 30.0000 chunk 184 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14053 Z= 0.289 Angle : 0.689 10.971 19110 Z= 0.334 Chirality : 0.045 0.392 2275 Planarity : 0.004 0.036 2416 Dihedral : 6.541 56.299 2139 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.48 % Favored : 92.47 % Rotamer: Outliers : 3.35 % Allowed : 19.13 % Favored : 77.51 % 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: 0.01 (0.21), residues: 1859 helix: 1.45 (0.17), residues: 988 sheet: -0.54 (0.49), residues: 134 loop : -1.97 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 474 HIS 0.005 0.001 HIS A 471 PHE 0.028 0.002 PHE A 365 TYR 0.022 0.002 TYR A 890 ARG 0.003 0.000 ARG B 734 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.7724 (t70) REVERT: A 139 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7636 (ptp-110) REVERT: A 258 MET cc_start: 0.9235 (ttm) cc_final: 0.8962 (tmm) REVERT: A 288 LYS cc_start: 0.9380 (ptmm) cc_final: 0.9043 (ptpp) REVERT: A 296 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6608 (tm-30) REVERT: A 319 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7489 (tp) REVERT: A 337 MET cc_start: 0.8963 (mmm) cc_final: 0.8487 (mmm) REVERT: A 376 MET cc_start: 0.9165 (mmp) cc_final: 0.8962 (mmm) REVERT: A 430 MET cc_start: 0.8726 (tpt) cc_final: 0.8378 (tpt) REVERT: A 754 MET cc_start: 0.6693 (mpt) cc_final: 0.5993 (mmp) REVERT: A 984 MET cc_start: 0.8395 (tpp) cc_final: 0.8146 (tpp) REVERT: B 274 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9006 (p) REVERT: B 290 MET cc_start: 0.8537 (ptm) cc_final: 0.8295 (ptm) REVERT: B 458 MET cc_start: 0.9075 (tpp) cc_final: 0.8590 (tpp) REVERT: B 538 MET cc_start: 0.8818 (ttp) cc_final: 0.8543 (ttp) REVERT: B 592 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8502 (mm) REVERT: B 742 LEU cc_start: 0.8538 (mt) cc_final: 0.8322 (mt) REVERT: B 775 MET cc_start: 0.8730 (tpp) cc_final: 0.8194 (tpt) REVERT: B 829 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8167 (tt) outliers start: 48 outliers final: 41 residues processed: 192 average time/residue: 0.1979 time to fit residues: 61.3782 Evaluate side-chains 196 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.0050 chunk 44 optimal weight: 0.0370 chunk 135 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 27 optimal weight: 0.0770 chunk 129 optimal weight: 7.9990 overall best weight: 2.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074553 restraints weight = 49389.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076435 restraints weight = 23735.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077639 restraints weight = 14557.876| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14053 Z= 0.162 Angle : 0.627 10.624 19110 Z= 0.301 Chirality : 0.042 0.384 2275 Planarity : 0.004 0.038 2416 Dihedral : 6.218 57.255 2139 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 2.23 % Allowed : 20.11 % Favored : 77.65 % 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: 0.32 (0.21), residues: 1859 helix: 1.71 (0.17), residues: 977 sheet: -0.24 (0.50), residues: 130 loop : -1.82 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 474 HIS 0.004 0.001 HIS A 664 PHE 0.028 0.001 PHE A 365 TYR 0.012 0.001 TYR A 555 ARG 0.004 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.28 seconds wall clock time: 46 minutes 27.81 seconds (2787.81 seconds total)