Starting phenix.real_space_refine on Mon Mar 11 02:06:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/03_2024/8drn_27678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/03_2024/8drn_27678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/03_2024/8drn_27678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/03_2024/8drn_27678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/03_2024/8drn_27678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drn_27678/03_2024/8drn_27678.pdb" } resolution = 4.12 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= 0.001 sd= 0.045 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 24 5.16 5 C 4234 2.51 5 N 1130 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 593": "OE1" <-> "OE2" Residue "F GLU 602": "OE1" <-> "OE2" Residue "F PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F GLU 724": "OE1" <-> "OE2" Residue "F GLU 770": "OE1" <-> "OE2" Residue "F GLU 798": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "F" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3257 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 17, 'TRANS': 386} Time building chain proxies: 3.91, per 1000 atoms: 0.59 Number of scatterers: 6578 At special positions: 0 Unit cell: (107.944, 76.504, 88.032, 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 24 16.00 O 1190 8.00 N 1130 7.00 C 4234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 33.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.507A pdb=" N TRP A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.723A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.635A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 4.238A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.911A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 589' Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.509A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.627A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.568A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.770A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.936A pdb=" N PHE A 728 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'F' and resid 401 through 409 removed outlier: 3.547A pdb=" N TRP F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 437 through 443 removed outlier: 3.921A pdb=" N PHE F 441 " --> pdb=" O PRO F 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 443 " --> pdb=" O THR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.946A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 492 Processing helix chain 'F' and resid 509 through 513 removed outlier: 3.833A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 538 removed outlier: 3.801A pdb=" N SER F 537 " --> pdb=" O THR F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.711A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 611 removed outlier: 4.098A pdb=" N PHE F 609 " --> pdb=" O PRO F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 636 removed outlier: 3.524A pdb=" N SER F 632 " --> pdb=" O GLU F 629 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.934A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.699A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 728 Processing helix chain 'F' and resid 745 through 749 removed outlier: 3.540A pdb=" N ILE F 748 " --> pdb=" O SER F 745 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY F 749 " --> pdb=" O PRO F 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 745 through 749' Processing helix chain 'F' and resid 768 through 772 removed outlier: 4.126A pdb=" N LEU F 771 " --> pdb=" O PRO F 768 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 772 " --> pdb=" O PRO F 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 768 through 772' Processing helix chain 'F' and resid 785 through 790 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.816A pdb=" N ALA F 802 " --> pdb=" O GLU F 798 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.638A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 474 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS A 501 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 521 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS A 552 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 523 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 618 through 620 Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668 removed outlier: 7.012A pdb=" N LEU A 667 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 735 through 737 removed outlier: 6.819A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 419 through 420 removed outlier: 5.701A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU F 594 " --> pdb=" O ASP F 618 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS F 620 " --> pdb=" O LEU F 594 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU F 596 " --> pdb=" O LYS F 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU F 688 " --> pdb=" O SER F 712 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE F 711 " --> pdb=" O LYS F 735 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 457 through 458 removed outlier: 6.568A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 142 hydrogen bonds defined for protein. 306 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: 1.91 Time building geometry restraints manager: 2.40 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: 1885 1.33 - 1.46: 912 1.46 - 1.58: 3861 1.58 - 1.70: 1 1.70 - 1.82: 34 Bond restraints: 6693 Sorted by residual: bond pdb=" N TRP F 645 " pdb=" CA TRP F 645 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.16e-02 7.43e+03 8.95e+00 bond pdb=" CA HIS F 573 " pdb=" CB HIS F 573 " ideal model delta sigma weight residual 1.526 1.564 -0.037 1.53e-02 4.27e+03 6.00e+00 bond pdb=" N ASP A 444 " pdb=" CA ASP A 444 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.28e-02 6.10e+03 5.91e+00 bond pdb=" N GLN A 570 " pdb=" CA GLN A 570 " ideal model delta sigma weight residual 1.455 1.485 -0.031 1.37e-02 5.33e+03 4.97e+00 bond pdb=" N GLY F 523 " pdb=" CA GLY F 523 " ideal model delta sigma weight residual 1.449 1.480 -0.031 1.45e-02 4.76e+03 4.43e+00 ... (remaining 6688 not shown) Histogram of bond angle deviations from ideal: 97.17 - 104.64: 96 104.64 - 112.12: 3421 112.12 - 119.59: 2435 119.59 - 127.06: 3040 127.06 - 134.54: 70 Bond angle restraints: 9062 Sorted by residual: angle pdb=" CB MET F 432 " pdb=" CG MET F 432 " pdb=" SD MET F 432 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB GLU A 449 " pdb=" CG GLU A 449 " pdb=" CD GLU A 449 " ideal model delta sigma weight residual 112.60 119.20 -6.60 1.70e+00 3.46e-01 1.51e+01 angle pdb=" CA MET A 434 " pdb=" CB MET A 434 " pdb=" CG MET A 434 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LYS A 622 " pdb=" CB LYS A 622 " pdb=" CG LYS A 622 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA MET F 432 " pdb=" CB MET F 432 " pdb=" CG MET F 432 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 ... (remaining 9057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3644 17.88 - 35.76: 399 35.76 - 53.64: 95 53.64 - 71.52: 13 71.52 - 89.39: 5 Dihedral angle restraints: 4156 sinusoidal: 1754 harmonic: 2402 Sorted by residual: dihedral pdb=" CA LYS F 587 " pdb=" C LYS F 587 " pdb=" N MET F 588 " pdb=" CA MET F 588 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLU F 505 " pdb=" C GLU F 505 " pdb=" N LEU F 506 " pdb=" CA LEU F 506 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLU A 429 " pdb=" C GLU A 429 " pdb=" N LEU A 430 " pdb=" CA LEU A 430 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1027 0.098 - 0.195: 55 0.195 - 0.293: 1 0.293 - 0.390: 0 0.390 - 0.488: 1 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CB ILE A 629 " pdb=" CA ILE A 629 " pdb=" CG1 ILE A 629 " pdb=" CG2 ILE A 629 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CB ILE F 759 " pdb=" CA ILE F 759 " pdb=" CG1 ILE F 759 " pdb=" CG2 ILE F 759 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU A 723 " pdb=" CB LEU A 723 " pdb=" CD1 LEU A 723 " pdb=" CD2 LEU A 723 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1081 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.032 2.00e-02 2.50e+03 2.93e-02 2.15e+01 pdb=" CG TRP A 475 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 687 " -0.023 2.00e-02 2.50e+03 2.12e-02 8.95e+00 pdb=" CG TYR F 687 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR F 687 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR F 687 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR F 687 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 687 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR F 687 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 687 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 488 " -0.012 2.00e-02 2.50e+03 1.81e-02 5.72e+00 pdb=" CG PHE F 488 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE F 488 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE F 488 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE F 488 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 488 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 488 " -0.000 2.00e-02 2.50e+03 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1498 2.79 - 3.32: 6482 3.32 - 3.85: 11414 3.85 - 4.37: 14444 4.37 - 4.90: 22664 Nonbonded interactions: 56502 Sorted by model distance: nonbonded pdb=" OD1 ASP F 689 " pdb=" OG SER F 691 " model vdw 2.264 2.440 nonbonded pdb=" O LEU A 405 " pdb=" ND2 ASN A 409 " model vdw 2.285 2.520 nonbonded pdb=" O ARG A 419 " pdb=" NH1 ARG A 419 " model vdw 2.291 2.520 nonbonded pdb=" O GLN A 560 " pdb=" OG1 THR A 563 " model vdw 2.297 2.440 nonbonded pdb=" OE1 GLU A 429 " pdb=" NZ LYS A 452 " model vdw 2.297 2.520 ... (remaining 56497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.780 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.280 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 6693 Z= 0.285 Angle : 0.981 11.724 9062 Z= 0.510 Chirality : 0.050 0.488 1084 Planarity : 0.005 0.041 1137 Dihedral : 15.665 89.395 2580 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.26 % Allowed : 21.58 % Favored : 78.16 % 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: -2.70 (0.29), residues: 807 helix: -2.79 (0.28), residues: 248 sheet: -2.18 (0.53), residues: 113 loop : -0.96 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.006 TRP A 475 HIS 0.007 0.001 HIS F 669 PHE 0.041 0.002 PHE F 488 TYR 0.053 0.003 TYR F 687 ARG 0.006 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 280 time to evaluate : 0.988 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 404 GLN cc_start: 0.7410 (tm-30) cc_final: 0.7149 (tm-30) REVERT: A 414 ASP cc_start: 0.9263 (m-30) cc_final: 0.9055 (m-30) REVERT: A 454 GLU cc_start: 0.8379 (tt0) cc_final: 0.7941 (tm-30) REVERT: A 473 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8287 (tt0) REVERT: A 479 THR cc_start: 0.8730 (m) cc_final: 0.8258 (p) REVERT: A 518 LEU cc_start: 0.8894 (tp) cc_final: 0.8160 (tp) REVERT: A 547 LYS cc_start: 0.7844 (mttp) cc_final: 0.7594 (mptt) REVERT: A 601 CYS cc_start: 0.8010 (t) cc_final: 0.7640 (m) REVERT: A 624 ASN cc_start: 0.8450 (m-40) cc_final: 0.7962 (m110) REVERT: A 682 PHE cc_start: 0.8170 (m-80) cc_final: 0.7755 (m-80) REVERT: A 694 HIS cc_start: 0.8789 (m170) cc_final: 0.8582 (m170) REVERT: A 801 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7229 (tmt170) REVERT: A 803 TRP cc_start: 0.8431 (m100) cc_final: 0.8221 (m100) REVERT: F 421 ASN cc_start: 0.7637 (p0) cc_final: 0.7374 (p0) REVERT: F 486 LEU cc_start: 0.7943 (mt) cc_final: 0.7508 (tt) REVERT: F 503 MET cc_start: 0.7456 (mmt) cc_final: 0.6148 (tpp) REVERT: F 511 TYR cc_start: 0.7218 (m-80) cc_final: 0.6135 (m-80) REVERT: F 518 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6826 (mt-10) REVERT: F 567 LEU cc_start: 0.8318 (tp) cc_final: 0.7984 (tp) REVERT: F 588 MET cc_start: 0.7919 (mmp) cc_final: 0.7575 (mmm) REVERT: F 633 PHE cc_start: 0.8834 (m-80) cc_final: 0.8073 (m-80) REVERT: F 642 LEU cc_start: 0.7101 (tp) cc_final: 0.6216 (tt) REVERT: F 649 ILE cc_start: 0.8160 (mt) cc_final: 0.7051 (mm) REVERT: F 735 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7454 (mtmm) REVERT: F 756 TYR cc_start: 0.7701 (t80) cc_final: 0.6893 (t80) REVERT: F 764 PHE cc_start: 0.7230 (m-10) cc_final: 0.6911 (m-80) outliers start: 2 outliers final: 0 residues processed: 282 average time/residue: 0.2339 time to fit residues: 83.9615 Evaluate side-chains 181 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN A 650 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 706 GLN F 799 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6693 Z= 0.247 Angle : 0.739 10.407 9062 Z= 0.361 Chirality : 0.047 0.311 1084 Planarity : 0.005 0.077 1137 Dihedral : 5.276 19.059 864 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.13 % Allowed : 2.76 % Favored : 97.11 % 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: -2.47 (0.29), residues: 807 helix: -2.43 (0.30), residues: 237 sheet: -2.44 (0.50), residues: 119 loop : -0.83 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP F 645 HIS 0.007 0.001 HIS A 694 PHE 0.023 0.003 PHE A 433 TYR 0.023 0.003 TYR F 511 ARG 0.006 0.000 ARG F 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 0.855 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 404 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6949 (tm-30) REVERT: A 426 ASP cc_start: 0.9297 (m-30) cc_final: 0.9087 (t70) REVERT: A 475 TRP cc_start: 0.7524 (m-10) cc_final: 0.7185 (m-10) REVERT: A 518 LEU cc_start: 0.8521 (tp) cc_final: 0.8195 (tp) REVERT: A 557 LYS cc_start: 0.8377 (tptt) cc_final: 0.7599 (tmtt) REVERT: A 624 ASN cc_start: 0.8464 (m110) cc_final: 0.7942 (m-40) REVERT: A 645 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7555 (mtpp) REVERT: A 682 PHE cc_start: 0.8078 (m-80) cc_final: 0.7829 (m-80) REVERT: A 801 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7195 (tmt170) REVERT: F 432 MET cc_start: 0.7869 (mtm) cc_final: 0.7493 (tpt) REVERT: F 452 GLU cc_start: 0.8152 (tp30) cc_final: 0.7370 (tp30) REVERT: F 501 ASP cc_start: 0.8125 (t0) cc_final: 0.7859 (m-30) REVERT: F 503 MET cc_start: 0.6808 (mmt) cc_final: 0.6481 (tpp) REVERT: F 550 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7417 (mttm) REVERT: F 570 MET cc_start: 0.7950 (mmm) cc_final: 0.7525 (mmm) REVERT: F 573 HIS cc_start: 0.7829 (m170) cc_final: 0.7471 (m170) REVERT: F 581 MET cc_start: 0.6740 (tpt) cc_final: 0.6513 (tpt) REVERT: F 588 MET cc_start: 0.8216 (mmp) cc_final: 0.7544 (mmm) REVERT: F 633 PHE cc_start: 0.8480 (m-80) cc_final: 0.7783 (m-80) REVERT: F 642 LEU cc_start: 0.7027 (tp) cc_final: 0.6315 (tt) REVERT: F 644 LEU cc_start: 0.8885 (mt) cc_final: 0.8423 (mt) REVERT: F 645 TRP cc_start: 0.7454 (p90) cc_final: 0.7145 (p90) REVERT: F 726 TYR cc_start: 0.6720 (m-80) cc_final: 0.6485 (m-80) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1861 time to fit residues: 52.2309 Evaluate side-chains 152 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 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 431 HIS A 576 ASN A 657 GLN A 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6693 Z= 0.220 Angle : 0.698 8.593 9062 Z= 0.339 Chirality : 0.046 0.248 1084 Planarity : 0.004 0.038 1137 Dihedral : 5.011 17.253 864 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.92 % 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: -2.46 (0.29), residues: 807 helix: -2.23 (0.31), residues: 242 sheet: -2.82 (0.47), residues: 122 loop : -0.77 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 475 HIS 0.007 0.001 HIS A 694 PHE 0.017 0.002 PHE F 666 TYR 0.023 0.003 TYR F 687 ARG 0.003 0.000 ARG F 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 0.608 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 518 LEU cc_start: 0.8442 (tp) cc_final: 0.8208 (tp) REVERT: A 666 ARG cc_start: 0.7675 (mtp85) cc_final: 0.6989 (mtm180) REVERT: A 682 PHE cc_start: 0.8212 (m-80) cc_final: 0.7917 (m-80) REVERT: A 799 LYS cc_start: 0.8330 (pttm) cc_final: 0.8066 (ptpt) REVERT: A 801 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7304 (tmt170) REVERT: F 403 LEU cc_start: 0.8648 (tt) cc_final: 0.8402 (mm) REVERT: F 432 MET cc_start: 0.7945 (mtm) cc_final: 0.7250 (tpt) REVERT: F 452 GLU cc_start: 0.8215 (tp30) cc_final: 0.7951 (tp30) REVERT: F 503 MET cc_start: 0.6778 (mmt) cc_final: 0.6494 (tpp) REVERT: F 550 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7611 (mttm) REVERT: F 570 MET cc_start: 0.8086 (mmm) cc_final: 0.7548 (mmm) REVERT: F 573 HIS cc_start: 0.7680 (m170) cc_final: 0.7396 (m170) REVERT: F 588 MET cc_start: 0.8391 (mmp) cc_final: 0.7838 (mmm) REVERT: F 594 LEU cc_start: 0.9357 (tp) cc_final: 0.8399 (tp) REVERT: F 595 GLU cc_start: 0.8625 (mt-10) cc_final: 0.7920 (mm-30) REVERT: F 616 GLU cc_start: 0.8603 (pt0) cc_final: 0.7902 (pp20) REVERT: F 642 LEU cc_start: 0.7312 (tp) cc_final: 0.6695 (tt) REVERT: F 644 LEU cc_start: 0.8560 (mt) cc_final: 0.8199 (mt) REVERT: F 687 TYR cc_start: 0.8272 (t80) cc_final: 0.7743 (t80) REVERT: F 706 GLN cc_start: 0.6272 (tp-100) cc_final: 0.5916 (tp-100) REVERT: F 726 TYR cc_start: 0.6366 (m-80) cc_final: 0.6109 (m-80) REVERT: F 759 ILE cc_start: 0.7557 (pt) cc_final: 0.7165 (pt) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1728 time to fit residues: 43.4935 Evaluate side-chains 143 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6693 Z= 0.196 Angle : 0.657 10.812 9062 Z= 0.318 Chirality : 0.046 0.263 1084 Planarity : 0.004 0.049 1137 Dihedral : 4.751 15.246 864 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.13 % Allowed : 2.11 % Favored : 97.76 % 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: -2.26 (0.30), residues: 807 helix: -2.05 (0.32), residues: 246 sheet: -2.31 (0.46), residues: 137 loop : -0.70 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP F 645 HIS 0.005 0.001 HIS A 694 PHE 0.017 0.002 PHE F 764 TYR 0.023 0.002 TYR F 511 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8856 (pm20) REVERT: A 473 GLU cc_start: 0.8562 (tt0) cc_final: 0.8118 (tt0) REVERT: A 518 LEU cc_start: 0.8517 (tp) cc_final: 0.8296 (tp) REVERT: A 557 LYS cc_start: 0.8129 (tptt) cc_final: 0.7030 (tmtt) REVERT: A 665 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 666 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7244 (mtm180) REVERT: A 682 PHE cc_start: 0.8163 (m-80) cc_final: 0.7928 (m-80) REVERT: A 801 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7247 (tmt170) REVERT: F 503 MET cc_start: 0.6795 (mmt) cc_final: 0.6296 (tpp) REVERT: F 567 LEU cc_start: 0.8552 (tp) cc_final: 0.8188 (tp) REVERT: F 570 MET cc_start: 0.8138 (mmm) cc_final: 0.7790 (mmm) REVERT: F 573 HIS cc_start: 0.7450 (m170) cc_final: 0.7236 (m170) REVERT: F 581 MET cc_start: 0.6745 (tpt) cc_final: 0.6450 (tpt) REVERT: F 588 MET cc_start: 0.8246 (mmp) cc_final: 0.7579 (mmm) REVERT: F 594 LEU cc_start: 0.9349 (tp) cc_final: 0.8436 (tp) REVERT: F 595 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7951 (mm-30) REVERT: F 616 GLU cc_start: 0.8463 (pt0) cc_final: 0.7867 (pp20) REVERT: F 687 TYR cc_start: 0.8249 (t80) cc_final: 0.7971 (t80) REVERT: F 764 PHE cc_start: 0.6863 (m-80) cc_final: 0.6498 (m-80) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1953 time to fit residues: 46.0572 Evaluate side-chains 139 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN ** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6693 Z= 0.249 Angle : 0.698 8.986 9062 Z= 0.345 Chirality : 0.048 0.257 1084 Planarity : 0.004 0.042 1137 Dihedral : 4.805 16.582 864 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: -2.02 (0.30), residues: 807 helix: -1.90 (0.32), residues: 240 sheet: -2.11 (0.46), residues: 143 loop : -0.53 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 647 HIS 0.004 0.001 HIS F 573 PHE 0.013 0.002 PHE F 488 TYR 0.031 0.003 TYR A 648 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8737 (tt0) cc_final: 0.7863 (tt0) REVERT: A 495 LEU cc_start: 0.8363 (tp) cc_final: 0.8111 (tt) REVERT: A 557 LYS cc_start: 0.8128 (tptt) cc_final: 0.7060 (tmtt) REVERT: A 624 ASN cc_start: 0.8648 (m110) cc_final: 0.8103 (m-40) REVERT: A 647 TRP cc_start: 0.6332 (p90) cc_final: 0.6081 (p90) REVERT: A 665 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 666 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7425 (mtm180) REVERT: A 740 ASN cc_start: 0.8737 (t0) cc_final: 0.8469 (t0) REVERT: A 801 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7376 (tmt170) REVERT: F 432 MET cc_start: 0.7902 (tpt) cc_final: 0.7229 (tpp) REVERT: F 503 MET cc_start: 0.7027 (mmt) cc_final: 0.6288 (tpp) REVERT: F 513 LEU cc_start: 0.8006 (mt) cc_final: 0.7668 (mt) REVERT: F 567 LEU cc_start: 0.8563 (tp) cc_final: 0.8126 (tp) REVERT: F 570 MET cc_start: 0.8057 (mmm) cc_final: 0.7562 (mmm) REVERT: F 573 HIS cc_start: 0.7587 (m170) cc_final: 0.7278 (m170) REVERT: F 581 MET cc_start: 0.6686 (tpt) cc_final: 0.6409 (tpt) REVERT: F 588 MET cc_start: 0.8302 (mmp) cc_final: 0.7697 (mmm) REVERT: F 594 LEU cc_start: 0.9403 (tp) cc_final: 0.8550 (tp) REVERT: F 595 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8035 (mm-30) REVERT: F 616 GLU cc_start: 0.8466 (pt0) cc_final: 0.7911 (pp20) REVERT: F 673 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6926 (pm20) REVERT: F 687 TYR cc_start: 0.8305 (t80) cc_final: 0.8069 (t80) REVERT: F 764 PHE cc_start: 0.6735 (m-80) cc_final: 0.6327 (m-80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1558 time to fit residues: 35.8647 Evaluate side-chains 128 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6693 Z= 0.191 Angle : 0.675 11.139 9062 Z= 0.324 Chirality : 0.047 0.231 1084 Planarity : 0.004 0.061 1137 Dihedral : 4.718 16.831 864 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -1.96 (0.30), residues: 807 helix: -1.89 (0.33), residues: 240 sheet: -1.95 (0.48), residues: 137 loop : -0.55 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 647 HIS 0.005 0.001 HIS F 573 PHE 0.020 0.002 PHE F 711 TYR 0.018 0.002 TYR F 756 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8779 (tt0) cc_final: 0.8036 (tt0) REVERT: A 518 LEU cc_start: 0.8527 (tp) cc_final: 0.8313 (tp) REVERT: A 557 LYS cc_start: 0.7979 (tptt) cc_final: 0.6954 (tmtt) REVERT: A 645 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7821 (ptmt) REVERT: A 647 TRP cc_start: 0.6778 (p90) cc_final: 0.5605 (p90) REVERT: A 665 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 682 PHE cc_start: 0.8281 (m-80) cc_final: 0.8062 (m-80) REVERT: A 740 ASN cc_start: 0.8764 (t0) cc_final: 0.8508 (t0) REVERT: A 801 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7411 (tmt170) REVERT: A 804 ARG cc_start: 0.7637 (ptm-80) cc_final: 0.7129 (mmp80) REVERT: F 486 LEU cc_start: 0.7349 (mt) cc_final: 0.7138 (mt) REVERT: F 503 MET cc_start: 0.6960 (mmt) cc_final: 0.6195 (tpp) REVERT: F 550 LYS cc_start: 0.8294 (mttt) cc_final: 0.7443 (mmtt) REVERT: F 567 LEU cc_start: 0.8686 (tp) cc_final: 0.8137 (tp) REVERT: F 570 MET cc_start: 0.8056 (mmm) cc_final: 0.7528 (mmm) REVERT: F 581 MET cc_start: 0.6755 (tpt) cc_final: 0.6483 (tpt) REVERT: F 588 MET cc_start: 0.8240 (mmp) cc_final: 0.7729 (mmm) REVERT: F 594 LEU cc_start: 0.9360 (tp) cc_final: 0.8509 (tp) REVERT: F 595 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8070 (mm-30) REVERT: F 616 GLU cc_start: 0.8463 (pt0) cc_final: 0.7871 (pp20) REVERT: F 764 PHE cc_start: 0.6615 (m-80) cc_final: 0.6095 (m-80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1816 time to fit residues: 40.1709 Evaluate side-chains 128 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6693 Z= 0.370 Angle : 0.807 10.303 9062 Z= 0.394 Chirality : 0.050 0.200 1084 Planarity : 0.005 0.056 1137 Dihedral : 5.198 15.990 864 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 31.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -2.18 (0.30), residues: 807 helix: -2.03 (0.32), residues: 241 sheet: -2.52 (0.44), residues: 137 loop : -0.54 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 647 HIS 0.007 0.001 HIS F 573 PHE 0.029 0.003 PHE A 443 TYR 0.038 0.003 TYR F 687 ARG 0.005 0.001 ARG F 664 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 473 GLU cc_start: 0.8777 (tt0) cc_final: 0.8065 (tt0) REVERT: A 557 LYS cc_start: 0.8108 (tptt) cc_final: 0.7047 (tmtt) REVERT: A 597 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7434 (mp0) REVERT: A 650 HIS cc_start: 0.7449 (m-70) cc_final: 0.6990 (m-70) REVERT: A 665 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 703 ASP cc_start: 0.8658 (m-30) cc_final: 0.8436 (m-30) REVERT: A 740 ASN cc_start: 0.8936 (t0) cc_final: 0.8697 (t0) REVERT: A 769 LEU cc_start: 0.8925 (mt) cc_final: 0.8696 (mt) REVERT: A 801 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7348 (tmt170) REVERT: F 449 LEU cc_start: 0.8771 (mm) cc_final: 0.8256 (mm) REVERT: F 486 LEU cc_start: 0.7462 (mt) cc_final: 0.7159 (mt) REVERT: F 503 MET cc_start: 0.7177 (mmt) cc_final: 0.6203 (tpp) REVERT: F 567 LEU cc_start: 0.8577 (tp) cc_final: 0.7983 (tp) REVERT: F 570 MET cc_start: 0.8264 (mmm) cc_final: 0.7659 (mmm) REVERT: F 581 MET cc_start: 0.7049 (tpt) cc_final: 0.6676 (tpt) REVERT: F 588 MET cc_start: 0.8324 (mmp) cc_final: 0.7831 (mmm) REVERT: F 594 LEU cc_start: 0.9393 (tp) cc_final: 0.8574 (tp) REVERT: F 595 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8278 (mm-30) REVERT: F 616 GLU cc_start: 0.8827 (pt0) cc_final: 0.8032 (pp20) REVERT: F 618 ASP cc_start: 0.7524 (t0) cc_final: 0.7000 (t0) REVERT: F 735 LYS cc_start: 0.8282 (mtmt) cc_final: 0.8053 (mtmm) REVERT: F 764 PHE cc_start: 0.7044 (m-80) cc_final: 0.6517 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1628 time to fit residues: 37.1975 Evaluate side-chains 124 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 0.0060 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN A 758 GLN ** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6693 Z= 0.226 Angle : 0.706 9.843 9062 Z= 0.342 Chirality : 0.048 0.199 1084 Planarity : 0.004 0.051 1137 Dihedral : 5.110 15.515 864 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -1.92 (0.30), residues: 807 helix: -1.90 (0.33), residues: 234 sheet: -1.93 (0.47), residues: 140 loop : -0.51 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.005 TRP A 647 HIS 0.005 0.001 HIS F 669 PHE 0.023 0.002 PHE F 666 TYR 0.021 0.002 TYR F 687 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 THR cc_start: 0.9088 (p) cc_final: 0.8871 (p) REVERT: A 429 GLU cc_start: 0.6239 (mp0) cc_final: 0.5986 (mp0) REVERT: A 473 GLU cc_start: 0.8718 (tt0) cc_final: 0.8190 (tt0) REVERT: A 557 LYS cc_start: 0.7938 (tptt) cc_final: 0.6931 (tmtt) REVERT: A 598 LEU cc_start: 0.7629 (mt) cc_final: 0.7232 (mm) REVERT: A 601 CYS cc_start: 0.8040 (m) cc_final: 0.7666 (m) REVERT: A 645 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7877 (mtmt) REVERT: A 647 TRP cc_start: 0.7449 (p90) cc_final: 0.6718 (p90) REVERT: A 665 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 740 ASN cc_start: 0.8874 (t0) cc_final: 0.8657 (t0) REVERT: A 801 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7278 (tmt170) REVERT: F 486 LEU cc_start: 0.7505 (mt) cc_final: 0.7221 (mt) REVERT: F 503 MET cc_start: 0.7191 (mmt) cc_final: 0.6189 (tpp) REVERT: F 510 MET cc_start: 0.8556 (pmm) cc_final: 0.8353 (pmm) REVERT: F 550 LYS cc_start: 0.8234 (mttt) cc_final: 0.7759 (mmtt) REVERT: F 570 MET cc_start: 0.8111 (mmm) cc_final: 0.7709 (mmp) REVERT: F 581 MET cc_start: 0.7089 (tpt) cc_final: 0.6647 (tpt) REVERT: F 588 MET cc_start: 0.8311 (mmp) cc_final: 0.7784 (mmm) REVERT: F 594 LEU cc_start: 0.9339 (tp) cc_final: 0.8524 (tp) REVERT: F 595 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8247 (mm-30) REVERT: F 616 GLU cc_start: 0.8680 (pt0) cc_final: 0.7908 (pp20) REVERT: F 618 ASP cc_start: 0.7352 (t0) cc_final: 0.6867 (t0) REVERT: F 643 LYS cc_start: 0.9059 (ptpp) cc_final: 0.8453 (ptpp) REVERT: F 764 PHE cc_start: 0.6810 (m-80) cc_final: 0.6172 (m-80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1656 time to fit residues: 36.8342 Evaluate side-chains 122 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6693 Z= 0.269 Angle : 0.739 10.523 9062 Z= 0.356 Chirality : 0.049 0.191 1084 Planarity : 0.005 0.050 1137 Dihedral : 5.232 19.109 864 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 27.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -2.07 (0.30), residues: 807 helix: -1.97 (0.33), residues: 235 sheet: -2.18 (0.46), residues: 137 loop : -0.58 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP A 647 HIS 0.005 0.001 HIS F 669 PHE 0.019 0.002 PHE F 666 TYR 0.026 0.003 TYR F 756 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 THR cc_start: 0.9031 (p) cc_final: 0.8764 (p) REVERT: A 473 GLU cc_start: 0.8736 (tt0) cc_final: 0.8216 (tt0) REVERT: A 557 LYS cc_start: 0.7958 (tptt) cc_final: 0.6971 (tmtt) REVERT: A 647 TRP cc_start: 0.7402 (p90) cc_final: 0.6719 (p90) REVERT: A 650 HIS cc_start: 0.7536 (m-70) cc_final: 0.7004 (m-70) REVERT: A 665 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 769 LEU cc_start: 0.9052 (mt) cc_final: 0.8840 (mt) REVERT: A 801 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7282 (tmt170) REVERT: F 486 LEU cc_start: 0.7472 (mt) cc_final: 0.7168 (mt) REVERT: F 503 MET cc_start: 0.7343 (mmt) cc_final: 0.6227 (tpp) REVERT: F 550 LYS cc_start: 0.8286 (mttt) cc_final: 0.7804 (mmtt) REVERT: F 570 MET cc_start: 0.8226 (mmm) cc_final: 0.7735 (mmm) REVERT: F 581 MET cc_start: 0.7185 (tpt) cc_final: 0.6738 (tpt) REVERT: F 588 MET cc_start: 0.8284 (mmp) cc_final: 0.7787 (mmm) REVERT: F 594 LEU cc_start: 0.9357 (tp) cc_final: 0.9044 (tp) REVERT: F 595 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8334 (mm-30) REVERT: F 616 GLU cc_start: 0.8732 (pt0) cc_final: 0.8418 (pt0) REVERT: F 618 ASP cc_start: 0.7631 (t0) cc_final: 0.6862 (t0) REVERT: F 643 LYS cc_start: 0.9121 (ptpp) cc_final: 0.8173 (ptpp) REVERT: F 644 LEU cc_start: 0.8936 (mt) cc_final: 0.8734 (tt) REVERT: F 764 PHE cc_start: 0.7002 (m-80) cc_final: 0.6414 (m-80) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1649 time to fit residues: 37.9350 Evaluate side-chains 121 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN A 758 GLN ** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6693 Z= 0.201 Angle : 0.716 10.852 9062 Z= 0.343 Chirality : 0.048 0.219 1084 Planarity : 0.004 0.047 1137 Dihedral : 5.121 17.128 864 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % 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: -1.98 (0.30), residues: 807 helix: -1.87 (0.32), residues: 247 sheet: -2.06 (0.47), residues: 137 loop : -0.53 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 475 HIS 0.008 0.001 HIS F 573 PHE 0.020 0.002 PHE F 666 TYR 0.015 0.002 TYR F 687 ARG 0.003 0.000 ARG A 762 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8731 (tt0) cc_final: 0.8185 (tt0) REVERT: A 557 LYS cc_start: 0.7912 (tptt) cc_final: 0.6904 (tmtt) REVERT: A 650 HIS cc_start: 0.7486 (m-70) cc_final: 0.6924 (m-70) REVERT: A 665 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 682 PHE cc_start: 0.8857 (m-10) cc_final: 0.8503 (m-80) REVERT: A 801 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7335 (tmt170) REVERT: F 486 LEU cc_start: 0.7379 (mt) cc_final: 0.7053 (mt) REVERT: F 503 MET cc_start: 0.7252 (mmt) cc_final: 0.6210 (tpp) REVERT: F 550 LYS cc_start: 0.8310 (mttt) cc_final: 0.7855 (mmtt) REVERT: F 570 MET cc_start: 0.8177 (mmm) cc_final: 0.7649 (mmm) REVERT: F 581 MET cc_start: 0.7138 (tpt) cc_final: 0.6718 (tpt) REVERT: F 588 MET cc_start: 0.8181 (mmp) cc_final: 0.7763 (mmm) REVERT: F 594 LEU cc_start: 0.9331 (tp) cc_final: 0.8965 (tp) REVERT: F 595 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8312 (mm-30) REVERT: F 618 ASP cc_start: 0.7387 (t0) cc_final: 0.6549 (t0) REVERT: F 643 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8380 (ptpp) REVERT: F 644 LEU cc_start: 0.8911 (mt) cc_final: 0.8657 (tt) REVERT: F 764 PHE cc_start: 0.6961 (m-80) cc_final: 0.6146 (m-80) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1641 time to fit residues: 36.5173 Evaluate side-chains 124 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0010 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.0770 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.115882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097779 restraints weight = 20105.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099899 restraints weight = 12557.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.102558 restraints weight = 8641.995| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6693 Z= 0.191 Angle : 0.699 10.037 9062 Z= 0.335 Chirality : 0.047 0.187 1084 Planarity : 0.004 0.046 1137 Dihedral : 5.047 18.014 864 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.86 (0.30), residues: 807 helix: -1.87 (0.33), residues: 235 sheet: -1.81 (0.46), residues: 150 loop : -0.43 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 475 HIS 0.005 0.001 HIS A 499 PHE 0.018 0.002 PHE F 666 TYR 0.021 0.002 TYR F 756 ARG 0.004 0.000 ARG A 781 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.07 seconds wall clock time: 38 minutes 27.73 seconds (2307.73 seconds total)