Starting phenix.real_space_refine on Mon Oct 14 00:45:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3t_44155/10_2024/9b3t_44155.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3t_44155/10_2024/9b3t_44155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3t_44155/10_2024/9b3t_44155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3t_44155/10_2024/9b3t_44155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3t_44155/10_2024/9b3t_44155.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3t_44155/10_2024/9b3t_44155.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10404 2.51 5 N 2840 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 16389 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2055 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 5 Chain: "B" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2052 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 5 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2004 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 6 Chain: "E" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2023 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 6 Chain: "F" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2084 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain breaks: 4 Chain: "G" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2104 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 5 Chain: "H" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2001 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 5 Time building chain proxies: 10.91, per 1000 atoms: 0.67 Number of scatterers: 16389 At special positions: 0 Unit cell: (130.68, 132.84, 88.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3045 8.00 N 2840 7.00 C 10404 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 - 3.00 Amino acid : True - 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: 4.21 Conformation dependent library (CDL) restraints added in 2.0 seconds 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.682A pdb=" N ILE A 383 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 404 removed outlier: 3.730A pdb=" N PHE A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TRP A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 432 removed outlier: 3.683A pdb=" N ALA A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.561A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 470 removed outlier: 3.616A pdb=" N ILE A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 500 removed outlier: 3.751A pdb=" N SER A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 516 Processing helix chain 'A' and resid 516 through 530 removed outlier: 4.236A pdb=" N PHE A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.769A pdb=" N GLN A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.872A pdb=" N LYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 630 removed outlier: 3.572A pdb=" N LEU A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 653 removed outlier: 3.910A pdb=" N TYR A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 385 removed outlier: 3.820A pdb=" N LEU B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Proline residue: B 379 - end of helix Processing helix chain 'B' and resid 390 through 404 removed outlier: 3.625A pdb=" N ASP B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 432 removed outlier: 3.585A pdb=" N PHE B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 470 removed outlier: 3.561A pdb=" N VAL B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 470 " --> pdb=" O GLN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 500 removed outlier: 4.140A pdb=" N VAL B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 530 removed outlier: 4.139A pdb=" N ARG B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 563 removed outlier: 3.693A pdb=" N ASP B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 560 " --> pdb=" O GLN B 556 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 591 removed outlier: 4.271A pdb=" N MET B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 587 through 591' Processing helix chain 'B' and resid 598 through 606 removed outlier: 3.547A pdb=" N SER B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 630 removed outlier: 3.534A pdb=" N GLU B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 657 removed outlier: 3.711A pdb=" N MET B 639 " --> pdb=" O THR B 635 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 669 removed outlier: 3.604A pdb=" N GLU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.641A pdb=" N ILE C 383 " --> pdb=" O PRO C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 404 removed outlier: 3.844A pdb=" N GLN C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 432 removed outlier: 3.519A pdb=" N PHE C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 446 Processing helix chain 'C' and resid 448 through 471 removed outlier: 3.596A pdb=" N ILE C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 500 removed outlier: 3.540A pdb=" N SER C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 486 " --> pdb=" O SER C 482 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 487 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 488 " --> pdb=" O MET C 484 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 516 Processing helix chain 'C' and resid 516 through 530 removed outlier: 4.220A pdb=" N PHE C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 521 " --> pdb=" O GLY C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 563 removed outlier: 3.727A pdb=" N ASN C 563 " --> pdb=" O ASP C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 593 Processing helix chain 'C' and resid 597 through 609 removed outlier: 3.509A pdb=" N LEU C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 629 removed outlier: 3.894A pdb=" N GLU C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 654 removed outlier: 3.736A pdb=" N ALA C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 651 " --> pdb=" O ARG C 647 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 653 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 654 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 672 removed outlier: 3.941A pdb=" N ARG C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 385 Processing helix chain 'D' and resid 390 through 401 removed outlier: 3.607A pdb=" N GLN D 394 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 432 removed outlier: 3.655A pdb=" N PHE D 430 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 447 through 470 removed outlier: 4.300A pdb=" N GLN D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 470 " --> pdb=" O GLN D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 500 removed outlier: 3.750A pdb=" N ILE D 483 " --> pdb=" O VAL D 479 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 530 removed outlier: 4.537A pdb=" N GLN D 518 " --> pdb=" O GLN D 514 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 562 removed outlier: 3.666A pdb=" N GLN D 556 " --> pdb=" O GLY D 552 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 557 " --> pdb=" O ARG D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 598 through 606 removed outlier: 3.802A pdb=" N SER D 606 " --> pdb=" O LEU D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 630 removed outlier: 3.707A pdb=" N VAL D 622 " --> pdb=" O GLN D 618 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 623 " --> pdb=" O LYS D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 654 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.613A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 385 removed outlier: 3.589A pdb=" N ILE E 383 " --> pdb=" O PRO E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 403 removed outlier: 3.536A pdb=" N TRP E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 432 removed outlier: 4.098A pdb=" N ALA E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 447 removed outlier: 4.020A pdb=" N ILE E 446 " --> pdb=" O SER E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 471 removed outlier: 3.635A pdb=" N ILE E 460 " --> pdb=" O ALA E 456 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 500 Processing helix chain 'E' and resid 504 through 516 Processing helix chain 'E' and resid 516 through 531 removed outlier: 4.287A pdb=" N PHE E 520 " --> pdb=" O THR E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 563 removed outlier: 3.536A pdb=" N GLN E 556 " --> pdb=" O GLY E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 592 removed outlier: 3.506A pdb=" N MET E 591 " --> pdb=" O ALA E 587 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.620A pdb=" N ASN E 603 " --> pdb=" O MET E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 624 removed outlier: 4.780A pdb=" N GLN E 620 " --> pdb=" O LEU E 616 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE E 621 " --> pdb=" O GLU E 617 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 623 " --> pdb=" O LYS E 619 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 624 " --> pdb=" O GLN E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 652 removed outlier: 3.970A pdb=" N ARG E 636 " --> pdb=" O LEU E 632 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY E 651 " --> pdb=" O ARG E 647 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG E 652 " --> pdb=" O ALA E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 672 Processing helix chain 'F' and resid 372 through 385 removed outlier: 3.832A pdb=" N LEU F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) Proline residue: F 379 - end of helix Processing helix chain 'F' and resid 391 through 403 removed outlier: 3.601A pdb=" N ASP F 401 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 433 removed outlier: 3.917A pdb=" N LYS F 412 " --> pdb=" O VAL F 408 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 447 Processing helix chain 'F' and resid 447 through 470 removed outlier: 4.297A pdb=" N GLN F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 453 " --> pdb=" O SER F 449 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE F 470 " --> pdb=" O GLN F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 500 removed outlier: 3.511A pdb=" N LEU F 486 " --> pdb=" O SER F 482 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE F 487 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 488 " --> pdb=" O MET F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 516 Processing helix chain 'F' and resid 516 through 530 removed outlier: 4.020A pdb=" N PHE F 520 " --> pdb=" O THR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 563 removed outlier: 3.630A pdb=" N GLY F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 557 " --> pdb=" O ARG F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 591 removed outlier: 4.246A pdb=" N MET F 591 " --> pdb=" O ALA F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 608 removed outlier: 3.801A pdb=" N GLY F 608 " --> pdb=" O VAL F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 630 removed outlier: 3.696A pdb=" N ILE F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 657 removed outlier: 3.694A pdb=" N TYR F 634 " --> pdb=" O LYS F 630 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 656 " --> pdb=" O ARG F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 669 removed outlier: 3.913A pdb=" N ARG F 665 " --> pdb=" O ASN F 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 385 Processing helix chain 'G' and resid 391 through 404 removed outlier: 3.711A pdb=" N ILE G 396 " --> pdb=" O ARG G 392 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 433 removed outlier: 3.510A pdb=" N ASP G 415 " --> pdb=" O GLY G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 469 removed outlier: 3.585A pdb=" N GLU G 469 " --> pdb=" O GLY G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 499 removed outlier: 3.836A pdb=" N VAL G 479 " --> pdb=" O SER G 475 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE G 487 " --> pdb=" O ILE G 483 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN G 488 " --> pdb=" O MET G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 516 Processing helix chain 'G' and resid 516 through 530 removed outlier: 4.164A pdb=" N PHE G 520 " --> pdb=" O THR G 516 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU G 527 " --> pdb=" O ALA G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 565 removed outlier: 3.765A pdb=" N VAL G 565 " --> pdb=" O TYR G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 594 removed outlier: 3.711A pdb=" N LYS G 594 " --> pdb=" O HIS G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 597 through 609 Processing helix chain 'G' and resid 615 through 629 removed outlier: 3.552A pdb=" N ILE G 626 " --> pdb=" O VAL G 622 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU G 627 " --> pdb=" O LEU G 623 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 628 " --> pdb=" O ASP G 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 630 through 654 removed outlier: 4.042A pdb=" N ARG G 636 " --> pdb=" O LEU G 632 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP G 641 " --> pdb=" O SER G 637 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY G 651 " --> pdb=" O ARG G 647 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU G 654 " --> pdb=" O ILE G 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 661 through 672 removed outlier: 4.400A pdb=" N ARG G 665 " --> pdb=" O ASN G 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 386 removed outlier: 3.968A pdb=" N MET H 386 " --> pdb=" O TYR H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 403 removed outlier: 4.270A pdb=" N TRP H 402 " --> pdb=" O ALA H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 432 removed outlier: 3.520A pdb=" N PHE H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 446 Processing helix chain 'H' and resid 447 through 471 removed outlier: 4.209A pdb=" N GLN H 451 " --> pdb=" O PHE H 447 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 452 " --> pdb=" O GLY H 448 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 461 " --> pdb=" O THR H 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE H 470 " --> pdb=" O GLN H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 499 removed outlier: 3.579A pdb=" N GLN H 488 " --> pdb=" O MET H 484 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 490 " --> pdb=" O LEU H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 530 removed outlier: 4.460A pdb=" N GLN H 518 " --> pdb=" O GLN H 514 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU H 519 " --> pdb=" O LYS H 515 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE H 520 " --> pdb=" O THR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 562 removed outlier: 3.523A pdb=" N GLN H 556 " --> pdb=" O GLY H 552 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN H 562 " --> pdb=" O ARG H 558 " (cutoff:3.500A) Processing helix chain 'H' and resid 587 through 591 removed outlier: 3.981A pdb=" N MET H 591 " --> pdb=" O ALA H 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 587 through 591' Processing helix chain 'H' and resid 598 through 606 removed outlier: 3.549A pdb=" N VAL H 604 " --> pdb=" O ALA H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 628 Processing helix chain 'H' and resid 630 through 657 removed outlier: 3.602A pdb=" N GLY H 651 " --> pdb=" O ARG H 647 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 657 " --> pdb=" O ILE H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 671 removed outlier: 3.626A pdb=" N LEU H 670 " --> pdb=" O LEU H 667 " (cutoff:3.500A) 1108 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4565 1.33 - 1.46: 2575 1.46 - 1.58: 9314 1.58 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 16643 Sorted by residual: bond pdb=" N ASP D 432 " pdb=" CA ASP D 432 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.26e-02 6.30e+03 8.45e+00 bond pdb=" N VAL B 638 " pdb=" CA VAL B 638 " ideal model delta sigma weight residual 1.463 1.496 -0.033 1.14e-02 7.69e+03 8.41e+00 bond pdb=" N ILE B 655 " pdb=" CA ILE B 655 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.15e+00 bond pdb=" N ASN B 661 " pdb=" CA ASN B 661 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.30e-02 5.92e+03 8.01e+00 bond pdb=" N VAL F 604 " pdb=" CA VAL F 604 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00 ... (remaining 16638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 21903 1.86 - 3.72: 451 3.72 - 5.58: 55 5.58 - 7.43: 17 7.43 - 9.29: 4 Bond angle restraints: 22430 Sorted by residual: angle pdb=" CA GLY H 473 " pdb=" C GLY H 473 " pdb=" O GLY H 473 " ideal model delta sigma weight residual 122.82 117.77 5.05 1.29e+00 6.01e-01 1.53e+01 angle pdb=" N TYR B 634 " pdb=" CA TYR B 634 " pdb=" C TYR B 634 " ideal model delta sigma weight residual 111.28 107.06 4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N PRO B 662 " pdb=" CA PRO B 662 " pdb=" CB PRO B 662 " ideal model delta sigma weight residual 103.25 99.65 3.60 1.05e+00 9.07e-01 1.17e+01 angle pdb=" N ASP F 393 " pdb=" CA ASP F 393 " pdb=" C ASP F 393 " ideal model delta sigma weight residual 111.07 107.43 3.64 1.07e+00 8.73e-01 1.15e+01 angle pdb=" CA GLU E 474 " pdb=" CB GLU E 474 " pdb=" CG GLU E 474 " ideal model delta sigma weight residual 114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01 ... (remaining 22425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8420 17.96 - 35.93: 1273 35.93 - 53.89: 354 53.89 - 71.86: 58 71.86 - 89.82: 29 Dihedral angle restraints: 10134 sinusoidal: 4175 harmonic: 5959 Sorted by residual: dihedral pdb=" CG ARG E 558 " pdb=" CD ARG E 558 " pdb=" NE ARG E 558 " pdb=" CZ ARG E 558 " ideal model delta sinusoidal sigma weight residual 90.00 44.54 45.46 2 1.50e+01 4.44e-03 1.08e+01 dihedral pdb=" CB GLU A 377 " pdb=" CG GLU A 377 " pdb=" CD GLU A 377 " pdb=" OE1 GLU A 377 " ideal model delta sinusoidal sigma weight residual 0.00 -89.82 89.82 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP F 407 " pdb=" CB ASP F 407 " pdb=" CG ASP F 407 " pdb=" OD1 ASP F 407 " ideal model delta sinusoidal sigma weight residual -30.00 -85.61 55.61 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 10131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1971 0.040 - 0.079: 505 0.079 - 0.119: 78 0.119 - 0.158: 14 0.158 - 0.198: 8 Chirality restraints: 2576 Sorted by residual: chirality pdb=" CA ILE B 655 " pdb=" N ILE B 655 " pdb=" C ILE B 655 " pdb=" CB ILE B 655 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA ILE B 650 " pdb=" N ILE B 650 " pdb=" C ILE B 650 " pdb=" CB ILE B 650 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA LEU B 657 " pdb=" N LEU B 657 " pdb=" C LEU B 657 " pdb=" CB LEU B 657 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 2573 not shown) Planarity restraints: 2851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 661 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C ASN A 661 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN A 661 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A 662 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 469 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C GLU H 469 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU H 469 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE H 470 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 502 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO A 503 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.025 5.00e-02 4.00e+02 ... (remaining 2848 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2602 2.75 - 3.29: 16539 3.29 - 3.83: 26548 3.83 - 4.36: 30510 4.36 - 4.90: 50687 Nonbonded interactions: 126886 Sorted by model distance: nonbonded pdb=" O TYR H 634 " pdb=" OG SER H 637 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU G 654 " pdb=" NH2 ARG G 665 " model vdw 2.217 3.120 nonbonded pdb=" O SER E 597 " pdb=" OG SER E 597 " model vdw 2.219 3.040 nonbonded pdb=" O TYR D 634 " pdb=" OG SER D 637 " model vdw 2.236 3.040 nonbonded pdb=" N GLU F 617 " pdb=" OE1 GLU F 617 " model vdw 2.242 3.120 ... (remaining 126881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \ ugh 563 or resid 587 through 591 or resid 597 through 608 or resid 616 through 6 \ 52 or resid 658 through 664 or (resid 665 and (name N or name CA or name C or na \ me O or name CB )) or resid 666 through 669)) selection = (chain 'B' and (resid 374 through 406 or resid 411 through 563 or resid 587 thro \ ugh 591 or resid 597 through 608 or resid 616 through 652 or resid 658 through 6 \ 69)) selection = (chain 'C' and (resid 374 through 406 or resid 411 through 563 or resid 587 thro \ ugh 591 or resid 597 through 608 or resid 616 through 652 or resid 658 through 6 \ 64 or (resid 665 and (name N or name CA or name C or name O or name CB )) or res \ id 666 through 669)) selection = (chain 'D' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \ ugh 563 or resid 587 through 591 or resid 597 through 608 or resid 616 through 6 \ 52 or resid 658 through 664 or (resid 665 and (name N or name CA or name C or na \ me O or name CB )) or resid 666 through 669)) selection = (chain 'E' and (resid 374 through 530 or resid 544 through 563 or resid 587 thro \ ugh 591 or resid 597 through 608 or resid 616 through 664 or (resid 665 and (nam \ e N or name CA or name C or name O or name CB )) or resid 666 through 669)) selection = (chain 'F' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \ ugh 563 or resid 587 through 591 or resid 597 through 608 or resid 616 through 6 \ 52 or resid 658 through 664 or (resid 665 and (name N or name CA or name C or na \ me O or name CB )) or resid 666 through 669)) selection = (chain 'G' and (resid 374 through 406 or resid 411 through 563 or resid 587 thro \ ugh 591 or resid 597 through 608 or resid 616 through 652 or resid 658 through 6 \ 64 or (resid 665 and (name N or name CA or name C or name O or name CB )) or res \ id 666 through 669)) selection = (chain 'H' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \ ugh 563 or resid 587 through 608 or resid 616 through 652 or resid 658 through 6 \ 64 or (resid 665 and (name N or name CA or name C or name O or name CB )) or res \ id 666 through 669)) } 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: 3.140 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 37.300 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.003 0.037 16643 Z= 0.220 Angle : 0.615 9.292 22430 Z= 0.359 Chirality : 0.037 0.198 2576 Planarity : 0.003 0.045 2851 Dihedral : 18.610 89.820 6240 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.81 % Allowed : 35.63 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 1953 helix: 0.66 (0.13), residues: 1543 sheet: None (None), residues: 0 loop : -1.30 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 496 HIS 0.004 0.001 HIS B 444 PHE 0.016 0.001 PHE G 470 TYR 0.008 0.001 TYR F 508 ARG 0.009 0.001 ARG E 558 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 502 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 492 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: B 507 GLU cc_start: 0.5969 (pt0) cc_final: 0.5589 (pt0) REVERT: D 643 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7769 (m-70) REVERT: E 447 PHE cc_start: 0.7958 (m-80) cc_final: 0.7729 (m-10) REVERT: E 589 ILE cc_start: 0.8668 (mm) cc_final: 0.8421 (tt) REVERT: E 618 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: F 386 MET cc_start: 0.7058 (mmm) cc_final: 0.5730 (mtp) REVERT: F 639 MET cc_start: 0.7798 (mmm) cc_final: 0.7050 (tpt) REVERT: G 555 PHE cc_start: 0.7893 (t80) cc_final: 0.7674 (t80) REVERT: G 599 MET cc_start: 0.7679 (mmm) cc_final: 0.7426 (mmm) REVERT: H 381 ASP cc_start: 0.7584 (t0) cc_final: 0.7380 (t0) REVERT: H 599 MET cc_start: 0.8415 (mmm) cc_final: 0.8104 (mmm) REVERT: H 603 ASN cc_start: 0.8466 (m110) cc_final: 0.8248 (m110) outliers start: 51 outliers final: 19 residues processed: 538 average time/residue: 0.3899 time to fit residues: 290.7608 Evaluate side-chains 310 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 288 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 643 HIS Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 618 GLN Chi-restraints excluded: chain E residue 658 ASP Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 619 LYS Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 633 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 183 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN A 661 ASN B 545 HIS B 590 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 598 HIS D 477 GLN D 514 GLN D 529 ASN ** D 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 ASN F 444 HIS F 556 GLN ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 444 HIS ** H 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16643 Z= 0.248 Angle : 0.691 9.388 22430 Z= 0.359 Chirality : 0.040 0.152 2576 Planarity : 0.005 0.052 2851 Dihedral : 4.964 53.194 2232 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.12 % Allowed : 30.01 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 1953 helix: 1.50 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -1.47 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 402 HIS 0.009 0.001 HIS H 590 PHE 0.016 0.002 PHE H 470 TYR 0.021 0.002 TYR D 508 ARG 0.010 0.001 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 321 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7596 (tpm170) REVERT: A 639 MET cc_start: 0.6829 (tpp) cc_final: 0.6397 (tpt) REVERT: B 386 MET cc_start: 0.7899 (mmp) cc_final: 0.7603 (mmp) REVERT: B 510 ARG cc_start: 0.7471 (tmm160) cc_final: 0.7222 (tmm-80) REVERT: B 556 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: B 639 MET cc_start: 0.7264 (mmm) cc_final: 0.6890 (mmm) REVERT: C 451 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: C 509 TYR cc_start: 0.7819 (m-10) cc_final: 0.7589 (m-10) REVERT: E 480 MET cc_start: 0.6131 (tpp) cc_final: 0.5717 (mpp) REVERT: H 377 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6131 (tm-30) outliers start: 93 outliers final: 35 residues processed: 395 average time/residue: 0.3603 time to fit residues: 201.1709 Evaluate side-chains 292 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 255 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 620 GLN Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 522 ILE Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 512 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 152 optimal weight: 0.0570 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN A 529 ASN A 661 ASN B 590 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 HIS D 445 ASN D 645 GLN E 598 HIS F 444 HIS F 556 GLN G 477 GLN G 514 GLN ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 ASN H 514 GLN ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16643 Z= 0.205 Angle : 0.641 12.975 22430 Z= 0.325 Chirality : 0.039 0.145 2576 Planarity : 0.004 0.061 2851 Dihedral : 4.001 29.299 2197 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.57 % Allowed : 29.02 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 1953 helix: 1.75 (0.13), residues: 1570 sheet: None (None), residues: 0 loop : -1.38 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 584 HIS 0.011 0.001 HIS F 444 PHE 0.013 0.001 PHE E 447 TYR 0.014 0.002 TYR H 634 ARG 0.011 0.001 ARG G 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 285 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 ARG cc_start: 0.7712 (tpp-160) cc_final: 0.7499 (tpm170) REVERT: A 661 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7792 (p0) REVERT: B 512 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8749 (tp) REVERT: B 556 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: C 468 MET cc_start: 0.6419 (mtm) cc_final: 0.5929 (mtm) REVERT: C 510 ARG cc_start: 0.7219 (tpt170) cc_final: 0.6739 (tpp-160) REVERT: D 414 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8398 (mtmm) REVERT: D 599 MET cc_start: 0.8335 (mmm) cc_final: 0.7981 (mmm) REVERT: F 386 MET cc_start: 0.7355 (mmm) cc_final: 0.7118 (mmm) REVERT: G 488 GLN cc_start: 0.7777 (tp40) cc_final: 0.7406 (tm-30) REVERT: G 599 MET cc_start: 0.7577 (mmm) cc_final: 0.7336 (mmm) REVERT: H 470 PHE cc_start: 0.5361 (m-80) cc_final: 0.5080 (m-80) outliers start: 83 outliers final: 32 residues processed: 351 average time/residue: 0.3488 time to fit residues: 177.6788 Evaluate side-chains 286 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 507 GLU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 631 SER Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain H residue 590 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 0.0020 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN A 661 ASN B 590 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 GLN D 645 GLN E 598 HIS F 400 ASN F 444 HIS ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16643 Z= 0.217 Angle : 0.632 10.728 22430 Z= 0.321 Chirality : 0.038 0.141 2576 Planarity : 0.004 0.043 2851 Dihedral : 3.847 25.579 2195 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.57 % Allowed : 28.91 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.19), residues: 1953 helix: 1.87 (0.13), residues: 1574 sheet: None (None), residues: 0 loop : -1.31 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 584 HIS 0.011 0.001 HIS H 590 PHE 0.059 0.002 PHE D 470 TYR 0.014 0.001 TYR B 634 ARG 0.006 0.000 ARG G 553 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 269 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 512 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8772 (tp) REVERT: B 556 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: C 510 ARG cc_start: 0.7225 (tpt170) cc_final: 0.6947 (tpp-160) REVERT: C 514 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7579 (mm-40) REVERT: D 511 MET cc_start: 0.8425 (tmm) cc_final: 0.8176 (tmm) REVERT: D 546 ARG cc_start: 0.6705 (ptt90) cc_final: 0.5633 (ptt-90) REVERT: D 599 MET cc_start: 0.8334 (mmm) cc_final: 0.7986 (mmm) REVERT: D 639 MET cc_start: 0.8640 (tpp) cc_final: 0.8416 (mmt) REVERT: E 549 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7491 (tpp80) REVERT: E 640 MET cc_start: 0.7825 (mmm) cc_final: 0.7608 (mmt) REVERT: F 640 MET cc_start: 0.6819 (mpp) cc_final: 0.6613 (mpp) REVERT: G 488 GLN cc_start: 0.7929 (tp40) cc_final: 0.7598 (tm-30) REVERT: G 599 MET cc_start: 0.7721 (mmm) cc_final: 0.6803 (mmm) REVERT: H 642 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8785 (tt) outliers start: 83 outliers final: 39 residues processed: 332 average time/residue: 0.3656 time to fit residues: 174.6300 Evaluate side-chains 289 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 247 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 618 GLN Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 507 GLU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 590 HIS Chi-restraints excluded: chain H residue 642 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN B 590 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 ASN D 477 GLN D 481 ASN D 556 GLN D 618 GLN D 645 GLN E 598 HIS F 444 HIS G 481 ASN ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 499 ASN ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 645 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16643 Z= 0.238 Angle : 0.634 10.065 22430 Z= 0.320 Chirality : 0.038 0.170 2576 Planarity : 0.004 0.046 2851 Dihedral : 3.768 20.360 2192 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.68 % Allowed : 29.07 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.19), residues: 1953 helix: 1.94 (0.13), residues: 1575 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 584 HIS 0.021 0.001 HIS G 593 PHE 0.042 0.002 PHE D 470 TYR 0.015 0.001 TYR H 634 ARG 0.011 0.001 ARG B 549 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 265 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 512 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8827 (tp) REVERT: B 550 LEU cc_start: 0.8761 (mt) cc_final: 0.7137 (mt) REVERT: B 556 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: B 670 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8152 (pp) REVERT: C 510 ARG cc_start: 0.7274 (tpt170) cc_final: 0.7043 (tpp-160) REVERT: C 514 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7446 (mm-40) REVERT: D 511 MET cc_start: 0.8603 (tmm) cc_final: 0.8377 (tmm) REVERT: D 599 MET cc_start: 0.8407 (mmm) cc_final: 0.8061 (mmm) REVERT: G 488 GLN cc_start: 0.7955 (tp40) cc_final: 0.7413 (tm-30) REVERT: G 492 MET cc_start: 0.8222 (mmm) cc_final: 0.7987 (mmp) REVERT: G 509 TYR cc_start: 0.8318 (m-10) cc_final: 0.7968 (m-80) REVERT: G 589 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8098 (mp) REVERT: G 599 MET cc_start: 0.7687 (mmm) cc_final: 0.6830 (mmm) REVERT: H 642 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8999 (tt) outliers start: 85 outliers final: 49 residues processed: 332 average time/residue: 0.3578 time to fit residues: 169.3999 Evaluate side-chains 298 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 244 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 555 PHE Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 507 GLU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 589 ILE Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 631 SER Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain G residue 670 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain H residue 557 ILE Chi-restraints excluded: chain H residue 590 HIS Chi-restraints excluded: chain H residue 642 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 38 optimal weight: 0.0030 chunk 114 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 195 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 529 ASN B 590 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 GLN D 645 GLN E 598 HIS F 444 HIS G 481 ASN ** G 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 645 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16643 Z= 0.198 Angle : 0.639 11.096 22430 Z= 0.317 Chirality : 0.038 0.340 2576 Planarity : 0.003 0.044 2851 Dihedral : 3.750 21.107 2192 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.02 % Allowed : 29.41 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1953 helix: 1.94 (0.13), residues: 1581 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 402 HIS 0.010 0.001 HIS H 590 PHE 0.043 0.001 PHE D 470 TYR 0.023 0.001 TYR A 458 ARG 0.010 0.001 ARG B 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 265 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8940 (tt) REVERT: B 512 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8719 (tp) REVERT: B 556 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: C 451 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: C 510 ARG cc_start: 0.7230 (tpt170) cc_final: 0.6980 (tpp-160) REVERT: C 514 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7423 (mm-40) REVERT: D 511 MET cc_start: 0.8590 (tmm) cc_final: 0.8338 (tmm) REVERT: D 599 MET cc_start: 0.8410 (mmm) cc_final: 0.8034 (mmm) REVERT: E 511 MET cc_start: 0.8430 (tmm) cc_final: 0.8052 (tmm) REVERT: E 549 ARG cc_start: 0.7561 (tpp80) cc_final: 0.7339 (tpp80) REVERT: G 488 GLN cc_start: 0.7922 (tp40) cc_final: 0.7383 (tm-30) REVERT: G 492 MET cc_start: 0.8224 (mmm) cc_final: 0.7995 (mmp) REVERT: G 509 TYR cc_start: 0.8325 (m-10) cc_final: 0.8108 (m-10) outliers start: 73 outliers final: 48 residues processed: 325 average time/residue: 0.3453 time to fit residues: 161.3533 Evaluate side-chains 304 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 252 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 507 GLU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 631 SER Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain G residue 670 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain H residue 590 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 194 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN E 598 HIS F 444 HIS ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 603 ASN ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16643 Z= 0.208 Angle : 0.648 9.620 22430 Z= 0.321 Chirality : 0.038 0.292 2576 Planarity : 0.003 0.045 2851 Dihedral : 3.724 22.255 2192 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.91 % Allowed : 29.52 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 1953 helix: 2.03 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 584 HIS 0.010 0.001 HIS H 590 PHE 0.047 0.001 PHE D 470 TYR 0.022 0.001 TYR H 634 ARG 0.007 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 257 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 512 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8746 (tp) REVERT: B 556 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: C 510 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6987 (tpp-160) REVERT: C 514 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7405 (mm-40) REVERT: D 511 MET cc_start: 0.8572 (tmm) cc_final: 0.8371 (tmm) REVERT: G 488 GLN cc_start: 0.7973 (tp40) cc_final: 0.7219 (tm-30) REVERT: H 377 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6023 (tm-30) outliers start: 71 outliers final: 50 residues processed: 312 average time/residue: 0.3470 time to fit residues: 156.7349 Evaluate side-chains 295 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 242 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 631 SER Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain G residue 670 LEU Chi-restraints excluded: chain H residue 469 GLU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 590 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN A 643 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 GLN D 645 GLN E 598 HIS F 444 HIS G 477 GLN G 481 ASN ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16643 Z= 0.228 Angle : 0.645 10.603 22430 Z= 0.322 Chirality : 0.038 0.277 2576 Planarity : 0.003 0.045 2851 Dihedral : 3.708 23.621 2192 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.80 % Allowed : 29.63 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1953 helix: 2.06 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 584 HIS 0.009 0.001 HIS D 590 PHE 0.027 0.001 PHE D 470 TYR 0.026 0.002 TYR H 634 ARG 0.010 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 256 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 549 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7552 (tpp80) REVERT: B 512 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8747 (tp) REVERT: B 556 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: C 510 ARG cc_start: 0.7242 (tpt170) cc_final: 0.7039 (tpp-160) REVERT: D 511 MET cc_start: 0.8628 (tmm) cc_final: 0.8410 (tmm) REVERT: G 488 GLN cc_start: 0.8178 (tp40) cc_final: 0.7701 (tm-30) REVERT: H 377 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5451 (tm-30) REVERT: H 381 ASP cc_start: 0.7409 (m-30) cc_final: 0.6960 (m-30) outliers start: 69 outliers final: 51 residues processed: 310 average time/residue: 0.3484 time to fit residues: 155.6807 Evaluate side-chains 301 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 247 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 477 GLN Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 631 SER Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain G residue 670 LEU Chi-restraints excluded: chain H residue 469 GLU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 543 CYS Chi-restraints excluded: chain H residue 590 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.0970 chunk 186 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 HIS F 444 HIS ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16643 Z= 0.207 Angle : 0.671 12.286 22430 Z= 0.331 Chirality : 0.039 0.329 2576 Planarity : 0.004 0.081 2851 Dihedral : 3.781 24.902 2192 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.52 % Allowed : 30.45 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1953 helix: 2.02 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.97 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 402 HIS 0.013 0.001 HIS D 590 PHE 0.026 0.001 PHE C 430 TYR 0.035 0.002 TYR A 634 ARG 0.009 0.001 ARG H 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 255 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8974 (tt) REVERT: B 512 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8718 (tp) REVERT: B 556 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: D 511 MET cc_start: 0.8624 (tmm) cc_final: 0.8396 (tmm) REVERT: E 549 ARG cc_start: 0.7498 (tpp80) cc_final: 0.7223 (tpp80) REVERT: F 639 MET cc_start: 0.8087 (tpt) cc_final: 0.7796 (tpt) REVERT: G 488 GLN cc_start: 0.8192 (tp40) cc_final: 0.7821 (tm-30) REVERT: H 377 GLU cc_start: 0.6201 (tm-30) cc_final: 0.5444 (tm-30) REVERT: H 381 ASP cc_start: 0.7356 (m-30) cc_final: 0.6856 (m-30) outliers start: 64 outliers final: 51 residues processed: 305 average time/residue: 0.3551 time to fit residues: 157.3688 Evaluate side-chains 291 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 477 GLN Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 467 ILE Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 631 SER Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain G residue 670 LEU Chi-restraints excluded: chain H residue 469 GLU Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 543 CYS Chi-restraints excluded: chain H residue 590 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 0.0370 chunk 98 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 529 ASN A 643 HIS ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 563 ASN E 598 HIS F 444 HIS G 466 GLN ** G 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16643 Z= 0.218 Angle : 0.697 13.583 22430 Z= 0.344 Chirality : 0.039 0.316 2576 Planarity : 0.004 0.050 2851 Dihedral : 3.863 34.002 2192 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.36 % Allowed : 30.62 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.20), residues: 1953 helix: 1.96 (0.13), residues: 1580 sheet: None (None), residues: 0 loop : -0.83 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 402 HIS 0.022 0.001 HIS G 593 PHE 0.044 0.001 PHE F 470 TYR 0.038 0.002 TYR A 634 ARG 0.013 0.001 ARG E 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 252 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 512 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8720 (tp) REVERT: B 556 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: D 546 ARG cc_start: 0.6555 (ptt-90) cc_final: 0.5961 (ptt-90) REVERT: E 549 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7221 (tpp80) REVERT: G 488 GLN cc_start: 0.8194 (tp40) cc_final: 0.7845 (tm-30) REVERT: H 377 GLU cc_start: 0.6222 (tm-30) cc_final: 0.5474 (tm-30) REVERT: H 381 ASP cc_start: 0.7248 (m-30) cc_final: 0.6720 (m-30) outliers start: 61 outliers final: 51 residues processed: 301 average time/residue: 0.3428 time to fit residues: 150.7743 Evaluate side-chains 300 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 246 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 477 GLN Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 492 MET Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 615 THR Chi-restraints excluded: chain G residue 631 SER Chi-restraints excluded: chain G residue 650 ILE Chi-restraints excluded: chain G residue 670 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain H residue 543 CYS Chi-restraints excluded: chain H residue 590 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 44 optimal weight: 5.9990 chunk 160 optimal weight: 0.3980 chunk 67 optimal weight: 0.2980 chunk 164 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 529 ASN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN E 598 HIS F 444 HIS ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.092484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068204 restraints weight = 56115.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071094 restraints weight = 31003.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073025 restraints weight = 21651.408| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16643 Z= 0.201 Angle : 0.710 13.323 22430 Z= 0.350 Chirality : 0.039 0.338 2576 Planarity : 0.004 0.071 2851 Dihedral : 3.882 34.095 2192 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.25 % Allowed : 31.11 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.20), residues: 1953 helix: 1.94 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 402 HIS 0.011 0.001 HIS D 590 PHE 0.049 0.001 PHE F 470 TYR 0.052 0.002 TYR A 634 ARG 0.017 0.001 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.80 seconds wall clock time: 74 minutes 15.66 seconds (4455.66 seconds total)