Starting phenix.real_space_refine on Tue Feb 13 14:45:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7d_28903/02_2024/8f7d_28903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7d_28903/02_2024/8f7d_28903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7d_28903/02_2024/8f7d_28903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7d_28903/02_2024/8f7d_28903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7d_28903/02_2024/8f7d_28903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7d_28903/02_2024/8f7d_28903.pdb" } resolution = 4.2 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= 0.003 sd= 0.044 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-5238/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: 4.16, per 1000 atoms: 0.63 Number of scatterers: 6578 At special positions: 0 Unit cell: (110.04, 73.36, 82.792, 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: 2.52 Conformation dependent library (CDL) restraints added in 1.4 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, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.724A 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: 3.912A 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: 3.508A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.628A 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: 3.771A 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 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 437 through 443 removed outlier: 3.922A 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: 3.834A 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: 3.540A 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: 3.833A 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: 3.817A 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: 6.824A 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: 7.702A 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: 7.283A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.842A 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: 6.818A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.686A 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: 7.012A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.432A 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: 7.976A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 7.363A 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: 7.350A 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: 6.473A 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: 6.680A 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 148 hydrogen bonds defined for protein. 321 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: 1.75 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1913 1.34 - 1.46: 916 1.46 - 1.58: 3829 1.58 - 1.70: 1 1.70 - 1.82: 34 Bond restraints: 6693 Sorted by residual: bond pdb=" N ASN A 423 " pdb=" CA ASN A 423 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.47e+00 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 9.06e+00 bond pdb=" N THR A 412 " pdb=" CA THR A 412 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.87e+00 bond pdb=" N LYS A 422 " pdb=" CA LYS A 422 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.75e+00 bond pdb=" N LEU A 430 " pdb=" CA LEU A 430 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.36e+00 ... (remaining 6688 not shown) Histogram of bond angle deviations from ideal: 97.17 - 104.64: 96 104.64 - 112.11: 3418 112.11 - 119.59: 2467 119.59 - 127.06: 3009 127.06 - 134.53: 72 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 112.70 124.43 -11.73 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 114.10 121.60 -7.50 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 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA PHE A 433 " pdb=" C PHE A 433 " pdb=" O PHE A 433 " ideal model delta sigma weight residual 120.71 116.75 3.96 1.06e+00 8.90e-01 1.40e+01 ... (remaining 9057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3658 17.87 - 35.75: 389 35.75 - 53.62: 90 53.62 - 71.50: 14 71.50 - 89.37: 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 180.00 157.55 22.45 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 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA SER F 677 " pdb=" C SER F 677 " pdb=" N HIS F 678 " pdb=" CA HIS F 678 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1011 0.098 - 0.195: 71 0.195 - 0.293: 1 0.293 - 0.391: 0 0.391 - 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 5.96e+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 1.64e+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 7.12e-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 2.92e-02 2.13e+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 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " -0.000 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 2.11e-02 8.94e+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 5.71e+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: 1456 2.79 - 3.32: 6490 3.32 - 3.85: 11415 3.85 - 4.37: 14419 4.37 - 4.90: 22616 Nonbonded interactions: 56396 Sorted by model distance: nonbonded pdb=" OD1 ASP F 689 " pdb=" OG SER F 691 " model vdw 2.264 2.440 nonbonded pdb=" O GLN A 560 " pdb=" OG1 THR A 563 " model vdw 2.297 2.440 nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.320 2.520 nonbonded pdb=" O ARG F 775 " pdb=" NH1 ARG F 775 " model vdw 2.327 2.520 nonbonded pdb=" O THR F 640 " pdb=" N ARG F 664 " model vdw 2.334 2.520 ... (remaining 56391 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: 4.090 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: 15.130 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.210 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 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 : 0.005 0.102 6693 Z= 0.335 Angle : 0.997 11.731 9062 Z= 0.556 Chirality : 0.053 0.488 1084 Planarity : 0.005 0.041 1137 Dihedral : 15.553 89.372 2580 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.53 % Allowed : 20.79 % Favored : 78.68 % 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: -2.71 (0.28), residues: 807 helix: -2.79 (0.28), residues: 248 sheet: -2.12 (0.53), residues: 113 loop : -0.99 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.005 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 0.004 0.001 ARG A 671 *********************** 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 284 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 280 time to evaluate : 0.800 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: A 518 LEU cc_start: 0.8016 (tp) cc_final: 0.7760 (tp) REVERT: A 551 LEU cc_start: 0.8946 (mt) cc_final: 0.8682 (mm) REVERT: A 572 LEU cc_start: 0.8671 (tp) cc_final: 0.8408 (tp) REVERT: A 592 ASN cc_start: 0.8153 (m-40) cc_final: 0.7555 (t0) REVERT: A 645 LYS cc_start: 0.8899 (mttt) cc_final: 0.8550 (mttp) REVERT: A 703 ASP cc_start: 0.7274 (m-30) cc_final: 0.6877 (t0) REVERT: F 423 HIS cc_start: 0.7386 (m90) cc_final: 0.7132 (m-70) REVERT: F 430 LEU cc_start: 0.8000 (mt) cc_final: 0.7799 (mp) REVERT: F 446 LEU cc_start: 0.8320 (mt) cc_final: 0.8035 (mt) REVERT: F 476 GLN cc_start: 0.8630 (mp10) cc_final: 0.8280 (mp10) REVERT: F 496 LEU cc_start: 0.7806 (tp) cc_final: 0.7538 (tp) REVERT: F 524 SER cc_start: 0.6946 (p) cc_final: 0.6098 (p) REVERT: F 581 MET cc_start: 0.6333 (tpt) cc_final: 0.5908 (tpp) REVERT: F 598 HIS cc_start: 0.7199 (t-170) cc_final: 0.6853 (t-170) REVERT: F 666 PHE cc_start: 0.8759 (m-80) cc_final: 0.6929 (m-80) REVERT: F 715 CYS cc_start: 0.6487 (m) cc_final: 0.6146 (m) REVERT: F 726 TYR cc_start: 0.6646 (m-80) cc_final: 0.6253 (m-80) REVERT: F 784 VAL cc_start: 0.6124 (m) cc_final: 0.5588 (m) REVERT: F 800 MET cc_start: 0.3332 (tpt) cc_final: 0.2796 (mmt) outliers start: 4 outliers final: 0 residues processed: 282 average time/residue: 0.2351 time to fit residues: 82.3278 Evaluate side-chains 159 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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: 0.4980 chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.0370 chunk 72 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN A 576 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS F 407 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6693 Z= 0.240 Angle : 0.776 10.432 9062 Z= 0.379 Chirality : 0.047 0.198 1084 Planarity : 0.005 0.041 1137 Dihedral : 5.264 19.599 864 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % 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: -2.63 (0.29), residues: 807 helix: -2.65 (0.28), residues: 255 sheet: -2.66 (0.46), residues: 141 loop : -0.57 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.006 TRP A 803 HIS 0.015 0.002 HIS A 431 PHE 0.034 0.003 PHE F 609 TYR 0.023 0.003 TYR F 646 ARG 0.004 0.001 ARG A 765 *********************** 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 207 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.857 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: A 429 GLU cc_start: 0.8223 (pt0) cc_final: 0.8017 (pt0) REVERT: A 465 ILE cc_start: 0.8334 (tt) cc_final: 0.8117 (tt) REVERT: A 495 LEU cc_start: 0.8483 (tp) cc_final: 0.8247 (tp) REVERT: A 500 ILE cc_start: 0.8737 (mm) cc_final: 0.8485 (mp) REVERT: A 572 LEU cc_start: 0.8638 (tp) cc_final: 0.8191 (tp) REVERT: A 576 ASN cc_start: 0.9398 (m-40) cc_final: 0.9027 (t0) REVERT: A 592 ASN cc_start: 0.8320 (m-40) cc_final: 0.7842 (t0) REVERT: A 626 LEU cc_start: 0.8219 (tp) cc_final: 0.7999 (tp) REVERT: A 687 LEU cc_start: 0.8443 (mt) cc_final: 0.8146 (mt) REVERT: A 689 TYR cc_start: 0.8052 (m-80) cc_final: 0.7728 (m-80) REVERT: A 713 LEU cc_start: 0.8747 (tp) cc_final: 0.8039 (pp) REVERT: A 728 PHE cc_start: 0.8419 (m-80) cc_final: 0.7492 (m-80) REVERT: A 769 LEU cc_start: 0.8629 (mt) cc_final: 0.8220 (tp) REVERT: F 423 HIS cc_start: 0.7655 (m90) cc_final: 0.7218 (m-70) REVERT: F 446 LEU cc_start: 0.8289 (mt) cc_final: 0.7838 (mt) REVERT: F 573 HIS cc_start: 0.7863 (m90) cc_final: 0.7450 (m-70) REVERT: F 598 HIS cc_start: 0.7685 (t-170) cc_final: 0.7380 (t-170) REVERT: F 617 LEU cc_start: 0.7135 (tp) cc_final: 0.6670 (pp) REVERT: F 643 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8793 (tptp) REVERT: F 666 PHE cc_start: 0.9082 (m-80) cc_final: 0.7533 (m-10) REVERT: F 778 LYS cc_start: 0.4835 (mmmt) cc_final: 0.4501 (mmtm) REVERT: F 800 MET cc_start: 0.3492 (tpt) cc_final: 0.2965 (mmp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2252 time to fit residues: 59.7267 Evaluate side-chains 139 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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: 0.9980 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS F 416 GLN F 573 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6693 Z= 0.348 Angle : 0.872 11.981 9062 Z= 0.431 Chirality : 0.050 0.273 1084 Planarity : 0.006 0.041 1137 Dihedral : 5.669 23.963 864 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 31.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.13 % Allowed : 6.18 % Favored : 93.68 % 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: -2.91 (0.29), residues: 807 helix: -2.78 (0.27), residues: 258 sheet: -2.89 (0.44), residues: 146 loop : -0.73 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP F 645 HIS 0.008 0.002 HIS A 694 PHE 0.019 0.003 PHE A 635 TYR 0.017 0.003 TYR F 520 ARG 0.015 0.001 ARG A 492 *********************** 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 169 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 0.862 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: A 429 GLU cc_start: 0.8566 (pt0) cc_final: 0.8279 (pt0) REVERT: A 436 SER cc_start: 0.9182 (m) cc_final: 0.8870 (t) REVERT: A 473 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 549 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 576 ASN cc_start: 0.9424 (m-40) cc_final: 0.9085 (m-40) REVERT: A 713 LEU cc_start: 0.8901 (tp) cc_final: 0.7897 (pp) REVERT: F 403 LEU cc_start: 0.8350 (tt) cc_final: 0.7822 (mm) REVERT: F 446 LEU cc_start: 0.8345 (mt) cc_final: 0.8053 (mt) REVERT: F 454 ILE cc_start: 0.8615 (mp) cc_final: 0.8193 (tt) REVERT: F 598 HIS cc_start: 0.7521 (t-170) cc_final: 0.7269 (t-170) REVERT: F 617 LEU cc_start: 0.7079 (tp) cc_final: 0.6699 (pp) REVERT: F 800 MET cc_start: 0.3297 (tpt) cc_final: 0.2892 (mmp) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1972 time to fit residues: 44.0239 Evaluate side-chains 132 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.0370 chunk 64 optimal weight: 0.4980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 HIS ** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6693 Z= 0.207 Angle : 0.702 9.012 9062 Z= 0.348 Chirality : 0.045 0.156 1084 Planarity : 0.004 0.038 1137 Dihedral : 5.183 23.056 864 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.26 % Allowed : 3.82 % 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: -2.92 (0.29), residues: 807 helix: -2.68 (0.27), residues: 266 sheet: -2.84 (0.42), residues: 152 loop : -0.74 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP A 647 HIS 0.008 0.001 HIS F 606 PHE 0.015 0.002 PHE A 611 TYR 0.022 0.003 TYR F 710 ARG 0.004 0.000 ARG A 688 *********************** 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 163 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.778 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 429 GLU cc_start: 0.8403 (pt0) cc_final: 0.8164 (pt0) REVERT: A 436 SER cc_start: 0.8992 (m) cc_final: 0.8623 (t) REVERT: A 443 PHE cc_start: 0.8269 (m-10) cc_final: 0.8016 (m-80) REVERT: A 465 ILE cc_start: 0.8462 (tt) cc_final: 0.8038 (tp) REVERT: A 473 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 495 LEU cc_start: 0.8662 (tp) cc_final: 0.8459 (tp) REVERT: A 498 LEU cc_start: 0.9192 (mt) cc_final: 0.8673 (tp) REVERT: A 560 GLN cc_start: 0.6007 (OUTLIER) cc_final: 0.5692 (tm-30) REVERT: A 576 ASN cc_start: 0.9447 (m-40) cc_final: 0.9019 (t0) REVERT: A 595 GLU cc_start: 0.8398 (pm20) cc_final: 0.7464 (pm20) REVERT: A 713 LEU cc_start: 0.8849 (tp) cc_final: 0.7845 (pp) REVERT: A 760 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7614 (tm-30) REVERT: F 403 LEU cc_start: 0.8223 (tt) cc_final: 0.7705 (mm) REVERT: F 446 LEU cc_start: 0.8085 (mt) cc_final: 0.7848 (mt) REVERT: F 474 LEU cc_start: 0.8876 (mt) cc_final: 0.8572 (mt) REVERT: F 581 MET cc_start: 0.7086 (tpt) cc_final: 0.6174 (tpt) REVERT: F 598 HIS cc_start: 0.7493 (t-170) cc_final: 0.7228 (t-170) REVERT: F 666 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.7703 (m-10) REVERT: F 778 LYS cc_start: 0.5940 (mmtm) cc_final: 0.5355 (mmtm) REVERT: F 800 MET cc_start: 0.3140 (tpt) cc_final: 0.2608 (mmp) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.2064 time to fit residues: 43.3518 Evaluate side-chains 130 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6693 Z= 0.190 Angle : 0.689 9.321 9062 Z= 0.335 Chirality : 0.046 0.239 1084 Planarity : 0.004 0.042 1137 Dihedral : 5.007 22.810 864 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: -2.65 (0.30), residues: 807 helix: -2.61 (0.28), residues: 262 sheet: -2.54 (0.44), residues: 149 loop : -0.58 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.005 TRP A 803 HIS 0.006 0.001 HIS A 694 PHE 0.013 0.002 PHE F 666 TYR 0.034 0.003 TYR F 646 ARG 0.007 0.001 ARG A 492 *********************** 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 157 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.8294 (pt0) cc_final: 0.7801 (pm20) REVERT: A 436 SER cc_start: 0.8960 (m) cc_final: 0.8579 (t) REVERT: A 465 ILE cc_start: 0.8593 (tt) cc_final: 0.8130 (tp) REVERT: A 495 LEU cc_start: 0.8432 (tp) cc_final: 0.8031 (tp) REVERT: A 498 LEU cc_start: 0.9218 (mt) cc_final: 0.8688 (tp) REVERT: A 576 ASN cc_start: 0.9454 (m-40) cc_final: 0.8996 (t0) REVERT: A 668 TYR cc_start: 0.6262 (m-80) cc_final: 0.5199 (m-80) REVERT: A 713 LEU cc_start: 0.8805 (tp) cc_final: 0.7835 (pp) REVERT: F 426 LEU cc_start: 0.7536 (tp) cc_final: 0.7137 (tp) REVERT: F 573 HIS cc_start: 0.7839 (m-70) cc_final: 0.7596 (m-70) REVERT: F 598 HIS cc_start: 0.7399 (t-170) cc_final: 0.7065 (t-170) REVERT: F 666 PHE cc_start: 0.8840 (m-10) cc_final: 0.7725 (m-10) REVERT: F 759 ILE cc_start: 0.7733 (mm) cc_final: 0.7392 (mm) REVERT: F 778 LYS cc_start: 0.6161 (mmtm) cc_final: 0.5677 (mmtm) REVERT: F 800 MET cc_start: 0.2690 (tpt) cc_final: 0.2153 (mmt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1979 time to fit residues: 42.0628 Evaluate side-chains 119 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN F 482 HIS ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 6693 Z= 0.404 Angle : 0.904 13.677 9062 Z= 0.448 Chirality : 0.051 0.345 1084 Planarity : 0.006 0.059 1137 Dihedral : 5.847 26.508 864 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 34.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.28), residues: 807 helix: -3.02 (0.25), residues: 259 sheet: -2.46 (0.42), residues: 148 loop : -1.27 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.005 TRP F 645 HIS 0.010 0.002 HIS F 598 PHE 0.031 0.004 PHE A 443 TYR 0.016 0.003 TYR A 668 ARG 0.007 0.001 ARG A 533 *********************** 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 148 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.8174 (pt0) cc_final: 0.7829 (pt0) REVERT: A 436 SER cc_start: 0.9045 (m) cc_final: 0.8708 (t) REVERT: A 495 LEU cc_start: 0.8436 (tp) cc_final: 0.8218 (tp) REVERT: A 498 LEU cc_start: 0.9247 (mt) cc_final: 0.8820 (tp) REVERT: A 518 LEU cc_start: 0.8675 (tp) cc_final: 0.8119 (tp) REVERT: A 683 TYR cc_start: 0.7449 (t80) cc_final: 0.7221 (t80) REVERT: A 689 TYR cc_start: 0.8367 (m-80) cc_final: 0.8164 (m-80) REVERT: A 713 LEU cc_start: 0.8813 (tp) cc_final: 0.7765 (pp) REVERT: A 803 TRP cc_start: 0.7767 (m100) cc_final: 0.7512 (m100) REVERT: F 513 LEU cc_start: 0.7224 (mt) cc_final: 0.6700 (mp) REVERT: F 573 HIS cc_start: 0.7753 (m-70) cc_final: 0.7420 (m-70) REVERT: F 581 MET cc_start: 0.7404 (tpt) cc_final: 0.7007 (tpp) REVERT: F 659 LEU cc_start: 0.4392 (tp) cc_final: 0.4035 (tp) REVERT: F 778 LYS cc_start: 0.6300 (mmtm) cc_final: 0.5851 (mmtt) REVERT: F 800 MET cc_start: 0.2828 (tpt) cc_final: 0.2196 (mmt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1605 time to fit residues: 32.6922 Evaluate side-chains 107 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 HIS F 482 HIS ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.8228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6693 Z= 0.242 Angle : 0.742 9.884 9062 Z= 0.367 Chirality : 0.046 0.244 1084 Planarity : 0.005 0.062 1137 Dihedral : 5.513 27.551 864 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.29), residues: 807 helix: -2.81 (0.27), residues: 258 sheet: -2.48 (0.41), residues: 159 loop : -1.04 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.005 TRP A 647 HIS 0.010 0.001 HIS F 598 PHE 0.020 0.002 PHE F 667 TYR 0.037 0.003 TYR F 511 ARG 0.003 0.001 ARG F 415 *********************** 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 151 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 SER cc_start: 0.9056 (m) cc_final: 0.8778 (t) REVERT: A 498 LEU cc_start: 0.9235 (mt) cc_final: 0.8778 (tp) REVERT: A 518 LEU cc_start: 0.8100 (tp) cc_final: 0.7359 (tp) REVERT: A 571 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7668 (mmtm) REVERT: A 689 TYR cc_start: 0.8357 (m-80) cc_final: 0.8146 (m-80) REVERT: A 713 LEU cc_start: 0.8754 (tp) cc_final: 0.7710 (pp) REVERT: A 760 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7653 (tm-30) REVERT: F 439 THR cc_start: 0.8539 (t) cc_final: 0.8331 (t) REVERT: F 513 LEU cc_start: 0.7477 (mt) cc_final: 0.6980 (mp) REVERT: F 526 SER cc_start: 0.4977 (p) cc_final: 0.4680 (m) REVERT: F 573 HIS cc_start: 0.7873 (m-70) cc_final: 0.7579 (m-70) REVERT: F 581 MET cc_start: 0.7438 (tpt) cc_final: 0.7004 (tpp) REVERT: F 778 LYS cc_start: 0.6493 (mmtm) cc_final: 0.6028 (mmtt) REVERT: F 800 MET cc_start: 0.3357 (tpt) cc_final: 0.2812 (mmt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1701 time to fit residues: 35.1895 Evaluate side-chains 114 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 ASN F 598 HIS F 615 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.8607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6693 Z= 0.254 Angle : 0.735 10.783 9062 Z= 0.363 Chirality : 0.047 0.255 1084 Planarity : 0.005 0.055 1137 Dihedral : 5.500 27.125 864 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -3.08 (0.29), residues: 807 helix: -2.77 (0.28), residues: 258 sheet: -2.41 (0.42), residues: 158 loop : -1.17 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP A 647 HIS 0.007 0.001 HIS F 669 PHE 0.023 0.003 PHE F 667 TYR 0.027 0.002 TYR F 511 ARG 0.004 0.001 ARG F 686 *********************** 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 148 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.8821 (pt0) cc_final: 0.8335 (pt0) REVERT: A 436 SER cc_start: 0.9009 (m) cc_final: 0.8685 (t) REVERT: A 473 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 498 LEU cc_start: 0.9253 (mt) cc_final: 0.8775 (tp) REVERT: A 518 LEU cc_start: 0.8323 (tp) cc_final: 0.7617 (tp) REVERT: A 570 GLN cc_start: 0.9044 (mt0) cc_final: 0.8682 (mt0) REVERT: A 571 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7633 (mmtt) REVERT: A 595 GLU cc_start: 0.8684 (pm20) cc_final: 0.8260 (pm20) REVERT: A 686 LYS cc_start: 0.8260 (mttt) cc_final: 0.7536 (tptt) REVERT: A 689 TYR cc_start: 0.8433 (m-80) cc_final: 0.8181 (m-80) REVERT: A 713 LEU cc_start: 0.8750 (tp) cc_final: 0.7722 (pp) REVERT: A 760 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7568 (tm-30) REVERT: F 513 LEU cc_start: 0.7292 (mt) cc_final: 0.6809 (mp) REVERT: F 526 SER cc_start: 0.4997 (p) cc_final: 0.4699 (m) REVERT: F 581 MET cc_start: 0.7535 (tpt) cc_final: 0.7099 (tpp) REVERT: F 778 LYS cc_start: 0.6575 (mmtm) cc_final: 0.6194 (mmtt) REVERT: F 800 MET cc_start: 0.3717 (tpt) cc_final: 0.3248 (mmt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1562 time to fit residues: 32.0504 Evaluate side-chains 119 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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: 6.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.9336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6693 Z= 0.361 Angle : 0.885 12.729 9062 Z= 0.440 Chirality : 0.052 0.327 1084 Planarity : 0.006 0.059 1137 Dihedral : 6.099 34.742 864 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 33.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.80 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.29), residues: 807 helix: -3.07 (0.27), residues: 245 sheet: -2.34 (0.44), residues: 158 loop : -1.26 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.006 TRP F 645 HIS 0.026 0.002 HIS F 598 PHE 0.028 0.003 PHE F 764 TYR 0.036 0.003 TYR F 511 ARG 0.007 0.001 ARG A 403 *********************** 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 142 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.8914 (pt0) cc_final: 0.8389 (pt0) REVERT: A 436 SER cc_start: 0.9008 (m) cc_final: 0.8621 (t) REVERT: A 498 LEU cc_start: 0.9135 (mt) cc_final: 0.8764 (tp) REVERT: A 518 LEU cc_start: 0.8310 (tp) cc_final: 0.7853 (tp) REVERT: A 570 GLN cc_start: 0.9036 (mt0) cc_final: 0.8626 (mp10) REVERT: A 571 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7720 (mmtt) REVERT: A 595 GLU cc_start: 0.8495 (pm20) cc_final: 0.8174 (pm20) REVERT: A 686 LYS cc_start: 0.8478 (mttt) cc_final: 0.7818 (tptt) REVERT: A 687 LEU cc_start: 0.8940 (mt) cc_final: 0.8611 (mt) REVERT: A 713 LEU cc_start: 0.8765 (tp) cc_final: 0.7754 (pp) REVERT: F 439 THR cc_start: 0.8636 (t) cc_final: 0.8391 (t) REVERT: F 474 LEU cc_start: 0.8697 (mt) cc_final: 0.8477 (mt) REVERT: F 513 LEU cc_start: 0.7563 (mt) cc_final: 0.7139 (mp) REVERT: F 526 SER cc_start: 0.5288 (p) cc_final: 0.4954 (m) REVERT: F 581 MET cc_start: 0.7570 (tpt) cc_final: 0.6965 (tpp) REVERT: F 778 LYS cc_start: 0.6537 (mmtm) cc_final: 0.6308 (mmtt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1634 time to fit residues: 32.0203 Evaluate side-chains 109 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 0.6980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 HIS ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.9231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6693 Z= 0.183 Angle : 0.715 11.382 9062 Z= 0.353 Chirality : 0.047 0.260 1084 Planarity : 0.005 0.052 1137 Dihedral : 5.381 29.893 864 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -2.94 (0.29), residues: 807 helix: -2.66 (0.29), residues: 245 sheet: -2.24 (0.43), residues: 163 loop : -1.17 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP F 645 HIS 0.007 0.001 HIS A 694 PHE 0.017 0.002 PHE F 633 TYR 0.030 0.003 TYR F 511 ARG 0.003 0.001 ARG A 417 ********************** 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 158 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.8886 (pt0) cc_final: 0.8345 (pt0) REVERT: A 436 SER cc_start: 0.8850 (m) cc_final: 0.8423 (t) REVERT: A 504 ASP cc_start: 0.8645 (t0) cc_final: 0.8433 (m-30) REVERT: A 518 LEU cc_start: 0.8554 (tp) cc_final: 0.8342 (tp) REVERT: A 550 ARG cc_start: 0.7549 (ttt-90) cc_final: 0.7318 (mtp-110) REVERT: A 570 GLN cc_start: 0.8980 (mt0) cc_final: 0.8306 (mp10) REVERT: A 571 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7526 (mmtt) REVERT: A 592 ASN cc_start: 0.7723 (m110) cc_final: 0.7375 (t0) REVERT: A 595 GLU cc_start: 0.8492 (pm20) cc_final: 0.8243 (pm20) REVERT: A 686 LYS cc_start: 0.8270 (mttt) cc_final: 0.7803 (tptt) REVERT: A 687 LEU cc_start: 0.8815 (mt) cc_final: 0.8445 (mt) REVERT: A 713 LEU cc_start: 0.8696 (tp) cc_final: 0.7664 (pp) REVERT: A 760 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7515 (tm-30) REVERT: F 439 THR cc_start: 0.8593 (t) cc_final: 0.8368 (t) REVERT: F 513 LEU cc_start: 0.7351 (mt) cc_final: 0.6903 (mp) REVERT: F 579 LEU cc_start: 0.5194 (tp) cc_final: 0.4985 (tp) REVERT: F 581 MET cc_start: 0.7545 (tpt) cc_final: 0.6966 (tpp) REVERT: F 778 LYS cc_start: 0.6580 (mmtm) cc_final: 0.6260 (mmtt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1650 time to fit residues: 35.4666 Evaluate side-chains 125 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 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 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.122692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.108853 restraints weight = 27953.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.108281 restraints weight = 22117.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.108975 restraints weight = 16096.396| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.9337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6693 Z= 0.187 Angle : 0.712 10.995 9062 Z= 0.346 Chirality : 0.046 0.255 1084 Planarity : 0.005 0.064 1137 Dihedral : 5.242 29.112 864 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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: -2.80 (0.29), residues: 807 helix: -2.54 (0.30), residues: 244 sheet: -2.05 (0.42), residues: 166 loop : -1.13 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP F 645 HIS 0.006 0.001 HIS A 694 PHE 0.029 0.002 PHE F 667 TYR 0.019 0.002 TYR F 511 ARG 0.003 0.000 ARG A 734 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.32 seconds wall clock time: 37 minutes 4.01 seconds (2224.01 seconds total)