Starting phenix.real_space_refine on Sun Aug 4 09:35:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0a_43706/08_2024/8w0a_43706.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0a_43706/08_2024/8w0a_43706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0a_43706/08_2024/8w0a_43706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0a_43706/08_2024/8w0a_43706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0a_43706/08_2024/8w0a_43706.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0a_43706/08_2024/8w0a_43706.cif" } resolution = 3.2 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 66 5.16 5 C 6532 2.51 5 N 1708 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 208": "OD1" <-> "OD2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 775": "OE1" <-> "OE2" Residue "C PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10216 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4968 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 616} Chain breaks: 7 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 4968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4968 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 616} Chain breaks: 7 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 6.51, per 1000 atoms: 0.64 Number of scatterers: 10216 At special positions: 0 Unit cell: (165.98, 93.74, 82.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 14 15.00 O 1896 8.00 N 1708 7.00 C 6532 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: 3.86 Conformation dependent library (CDL) restraints added in 1.7 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 56.8% alpha, 6.1% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.616A pdb=" N LEU C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 removed outlier: 4.008A pdb=" N ALA C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.325A pdb=" N LEU C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 136 removed outlier: 3.907A pdb=" N LEU C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.145A pdb=" N GLU C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.628A pdb=" N SER C 183 " --> pdb=" O HIS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.568A pdb=" N LEU C 221 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY C 222 " --> pdb=" O HIS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 244 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.776A pdb=" N VAL C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.734A pdb=" N THR C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 removed outlier: 3.512A pdb=" N ASP C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.969A pdb=" N MET C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 4.169A pdb=" N LYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.693A pdb=" N GLU C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 432 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.904A pdb=" N SER C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 528 through 537 removed outlier: 3.538A pdb=" N ARG C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.765A pdb=" N THR C 552 " --> pdb=" O GLN C 548 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 554 " --> pdb=" O MET C 550 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 556 " --> pdb=" O THR C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.823A pdb=" N ALA C 561 " --> pdb=" O THR C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 592 removed outlier: 3.555A pdb=" N TRP C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 589 " --> pdb=" O CYS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.839A pdb=" N LEU C 619 " --> pdb=" O GLY C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 639 removed outlier: 3.849A pdb=" N LEU C 629 " --> pdb=" O PRO C 625 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 637 " --> pdb=" O ALA C 633 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET C 639 " --> pdb=" O LEU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 653 removed outlier: 3.735A pdb=" N LEU C 653 " --> pdb=" O HIS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 674 Processing helix chain 'C' and resid 677 through 686 removed outlier: 3.707A pdb=" N ARG C 682 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 730 removed outlier: 3.620A pdb=" N HIS C 716 " --> pdb=" O GLN C 712 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE C 719 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 720 " --> pdb=" O HIS C 716 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C 721 " --> pdb=" O LYS C 717 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 725 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C 727 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 728 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.798A pdb=" N ILE C 737 " --> pdb=" O PRO C 733 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN C 739 " --> pdb=" O ARG C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 768 removed outlier: 4.206A pdb=" N GLN C 749 " --> pdb=" O ARG C 745 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER C 750 " --> pdb=" O GLY C 746 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 752 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN C 753 " --> pdb=" O GLN C 749 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 761 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 762 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 780 removed outlier: 3.524A pdb=" N GLU C 775 " --> pdb=" O TRP C 771 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 776 " --> pdb=" O HIS C 772 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 777 " --> pdb=" O ASN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 787 removed outlier: 3.740A pdb=" N THR C 786 " --> pdb=" O GLN C 782 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 787 " --> pdb=" O LYS C 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.616A pdb=" N LEU A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 removed outlier: 4.009A pdb=" N ALA A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.326A pdb=" N LEU A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 136 removed outlier: 3.908A pdb=" N LEU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.144A pdb=" N GLU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.628A pdb=" N SER A 183 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.568A pdb=" N LEU A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 244 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.776A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.735A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 363 removed outlier: 3.512A pdb=" N ASP A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.970A pdb=" N MET A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 4.169A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.693A pdb=" N GLU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.905A pdb=" N SER A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.538A pdb=" N ARG A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.765A pdb=" N THR A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.823A pdb=" N ALA A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 592 removed outlier: 3.555A pdb=" N TRP A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.838A pdb=" N LEU A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.848A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.735A pdb=" N LEU A 653 " --> pdb=" O HIS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 677 through 686 removed outlier: 3.707A pdb=" N ARG A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.620A pdb=" N HIS A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 720 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 728 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.797A pdb=" N ILE A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 768 removed outlier: 4.207A pdb=" N GLN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 750 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 753 " --> pdb=" O GLN A 749 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 762 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 780 removed outlier: 3.524A pdb=" N GLU A 775 " --> pdb=" O TRP A 771 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 776 " --> pdb=" O HIS A 772 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.740A pdb=" N THR A 786 " --> pdb=" O GLN A 782 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 263 through 264 removed outlier: 6.425A pdb=" N LEU C 111 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASN C 110 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR C 283 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 112 " --> pdb=" O TYR C 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.094A pdb=" N PHE C 142 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 214 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 301 through 304 removed outlier: 6.421A pdb=" N VAL C 457 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU C 341 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 414 through 415 removed outlier: 7.444A pdb=" N ALA C 414 " --> pdb=" O ALA C 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 463 through 464 Processing sheet with id=AA6, first strand: chain 'C' and resid 595 through 596 Processing sheet with id=AA7, first strand: chain 'C' and resid 640 through 643 Processing sheet with id=AA8, first strand: chain 'A' and resid 263 through 264 removed outlier: 6.426A pdb=" N LEU A 111 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASN A 110 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N TYR A 283 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 112 " --> pdb=" O TYR A 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.093A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 214 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 304 removed outlier: 6.421A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 414 through 415 removed outlier: 7.444A pdb=" N ALA A 414 " --> pdb=" O ALA A 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AB4, first strand: chain 'A' and resid 595 through 596 352 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3222 1.34 - 1.46: 1698 1.46 - 1.58: 5376 1.58 - 1.70: 26 1.70 - 1.82: 104 Bond restraints: 10426 Sorted by residual: bond pdb=" O3' DT D 4 " pdb=" P DT D 5 " ideal model delta sigma weight residual 1.607 1.584 0.023 1.50e-02 4.44e+03 2.34e+00 bond pdb=" O3' DT B 4 " pdb=" P DT B 5 " ideal model delta sigma weight residual 1.607 1.584 0.023 1.50e-02 4.44e+03 2.34e+00 bond pdb=" O3' DT B 3 " pdb=" P DT B 4 " ideal model delta sigma weight residual 1.607 1.589 0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" O3' DT D 3 " pdb=" P DT D 4 " ideal model delta sigma weight residual 1.607 1.589 0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" CB ASN A 279 " pdb=" CG ASN A 279 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.11e-01 ... (remaining 10421 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.32: 377 107.32 - 114.03: 5972 114.03 - 120.75: 4433 120.75 - 127.47: 3271 127.47 - 134.18: 105 Bond angle restraints: 14158 Sorted by residual: angle pdb=" CA LEU C 273 " pdb=" CB LEU C 273 " pdb=" CG LEU C 273 " ideal model delta sigma weight residual 116.30 126.25 -9.95 3.50e+00 8.16e-02 8.08e+00 angle pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " pdb=" CG LEU A 273 " ideal model delta sigma weight residual 116.30 126.23 -9.93 3.50e+00 8.16e-02 8.06e+00 angle pdb=" C ASP A 336 " pdb=" N ASN A 337 " pdb=" CA ASN A 337 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.21e+00 angle pdb=" CB MET A 391 " pdb=" CG MET A 391 " pdb=" SD MET A 391 " ideal model delta sigma weight residual 112.70 120.71 -8.01 3.00e+00 1.11e-01 7.14e+00 angle pdb=" CB MET C 391 " pdb=" CG MET C 391 " pdb=" SD MET C 391 " ideal model delta sigma weight residual 112.70 120.69 -7.99 3.00e+00 1.11e-01 7.10e+00 ... (remaining 14153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 5019 17.45 - 34.91: 805 34.91 - 52.36: 288 52.36 - 69.81: 62 69.81 - 87.27: 14 Dihedral angle restraints: 6188 sinusoidal: 2516 harmonic: 3672 Sorted by residual: dihedral pdb=" CA PRO A 656 " pdb=" C PRO A 656 " pdb=" N MET A 657 " pdb=" CA MET A 657 " ideal model delta harmonic sigma weight residual 180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO C 656 " pdb=" C PRO C 656 " pdb=" N MET C 657 " pdb=" CA MET C 657 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA MET A 657 " pdb=" C MET A 657 " pdb=" N PHE A 658 " pdb=" CA PHE A 658 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1131 0.035 - 0.070: 402 0.070 - 0.105: 93 0.105 - 0.140: 30 0.140 - 0.175: 4 Chirality restraints: 1660 Sorted by residual: chirality pdb=" CB ILE C 261 " pdb=" CA ILE C 261 " pdb=" CG1 ILE C 261 " pdb=" CG2 ILE C 261 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CB THR C 235 " pdb=" CA THR C 235 " pdb=" OG1 THR C 235 " pdb=" CG2 THR C 235 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 1657 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 781 " 0.007 2.00e-02 2.50e+03 1.48e-02 3.82e+00 pdb=" CG PHE A 781 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 781 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 781 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 781 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 781 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 781 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 781 " 0.007 2.00e-02 2.50e+03 1.47e-02 3.80e+00 pdb=" CG PHE C 781 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 781 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 781 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 781 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 781 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 781 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 279 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ASN A 279 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN A 279 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A 280 " 0.008 2.00e-02 2.50e+03 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 4 2.23 - 2.90: 4052 2.90 - 3.56: 14094 3.56 - 4.23: 22123 4.23 - 4.90: 37741 Nonbonded interactions: 78014 Sorted by model distance: nonbonded pdb=" ND2 ASN C 773 " pdb=" O LEU A 644 " model vdw 1.561 3.120 nonbonded pdb=" O LEU C 644 " pdb=" ND2 ASN A 773 " model vdw 1.566 3.120 nonbonded pdb=" CD1 LEU C 776 " pdb=" NE2 GLN A 780 " model vdw 1.935 3.540 nonbonded pdb=" NE2 GLN C 780 " pdb=" CD1 LEU A 776 " model vdw 1.940 3.540 nonbonded pdb=" ND2 ASN A 110 " pdb=" O LEU A 278 " model vdw 2.252 3.120 ... (remaining 78009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic 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: 5.250 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.410 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10426 Z= 0.174 Angle : 0.593 9.952 14158 Z= 0.309 Chirality : 0.040 0.175 1660 Planarity : 0.003 0.029 1720 Dihedral : 19.614 87.266 3808 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.09 % Allowed : 36.76 % Favored : 63.15 % 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: -1.76 (0.24), residues: 1240 helix: -0.95 (0.21), residues: 596 sheet: -2.43 (0.66), residues: 68 loop : -1.10 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 277 HIS 0.002 0.001 HIS A 219 PHE 0.032 0.001 PHE A 781 TYR 0.011 0.001 TYR A 283 ARG 0.002 0.000 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 ASP cc_start: 0.3212 (m-30) cc_final: 0.2381 (p0) REVERT: C 538 ILE cc_start: 0.6187 (pt) cc_final: 0.5882 (pt) REVERT: A 402 ASP cc_start: 0.3275 (m-30) cc_final: 0.2469 (p0) REVERT: A 538 ILE cc_start: 0.6177 (pt) cc_final: 0.5894 (pt) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.2302 time to fit residues: 46.5263 Evaluate side-chains 112 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN C 744 ASN C 749 GLN C 752 GLN A 260 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN A 749 GLN A 752 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10426 Z= 0.188 Angle : 0.575 5.634 14158 Z= 0.307 Chirality : 0.041 0.146 1660 Planarity : 0.004 0.030 1720 Dihedral : 10.612 87.291 1486 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.26 % Allowed : 33.89 % Favored : 61.85 % 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: -2.00 (0.23), residues: 1240 helix: -1.03 (0.19), residues: 662 sheet: -1.38 (0.51), residues: 118 loop : -1.52 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.006 0.001 HIS A 716 PHE 0.037 0.002 PHE A 87 TYR 0.010 0.001 TYR A 228 ARG 0.004 0.001 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6962 (mp) REVERT: C 402 ASP cc_start: 0.3278 (m-30) cc_final: 0.2482 (p0) REVERT: C 463 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5766 (tt) REVERT: C 538 ILE cc_start: 0.6112 (pt) cc_final: 0.5822 (pt) REVERT: A 388 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6945 (mp) REVERT: A 402 ASP cc_start: 0.3336 (m-30) cc_final: 0.2576 (p0) REVERT: A 463 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5724 (tt) REVERT: A 538 ILE cc_start: 0.6022 (pt) cc_final: 0.5728 (pt) REVERT: A 749 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7500 (pt0) outliers start: 46 outliers final: 24 residues processed: 166 average time/residue: 0.1988 time to fit residues: 48.0604 Evaluate side-chains 136 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 596 GLN Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 749 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN A 749 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10426 Z= 0.233 Angle : 0.586 8.963 14158 Z= 0.309 Chirality : 0.041 0.143 1660 Planarity : 0.004 0.030 1720 Dihedral : 10.568 87.974 1486 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.00 % Allowed : 32.69 % Favored : 62.31 % 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: -2.01 (0.23), residues: 1240 helix: -1.04 (0.19), residues: 666 sheet: -1.41 (0.50), residues: 118 loop : -1.51 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 771 HIS 0.003 0.001 HIS C 416 PHE 0.037 0.002 PHE C 87 TYR 0.011 0.001 TYR A 228 ARG 0.004 0.001 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 127 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6848 (ttm) REVERT: C 402 ASP cc_start: 0.3371 (m-30) cc_final: 0.2562 (p0) REVERT: A 212 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6864 (ttm) REVERT: A 402 ASP cc_start: 0.3322 (m-30) cc_final: 0.2562 (p0) REVERT: A 463 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5801 (tt) outliers start: 54 outliers final: 33 residues processed: 170 average time/residue: 0.1810 time to fit residues: 46.1050 Evaluate side-chains 147 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 ASN C 747 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10426 Z= 0.193 Angle : 0.551 5.363 14158 Z= 0.292 Chirality : 0.040 0.147 1660 Planarity : 0.004 0.031 1720 Dihedral : 10.450 89.204 1486 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.74 % Allowed : 33.15 % Favored : 61.11 % 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: -1.90 (0.23), residues: 1240 helix: -0.94 (0.19), residues: 670 sheet: -1.40 (0.50), residues: 118 loop : -1.47 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 95 HIS 0.004 0.001 HIS C 225 PHE 0.041 0.002 PHE A 87 TYR 0.009 0.001 TYR A 474 ARG 0.003 0.000 ARG C 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 116 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 388 LEU cc_start: 0.7099 (tp) cc_final: 0.6851 (mp) REVERT: C 402 ASP cc_start: 0.3340 (m-30) cc_final: 0.2548 (p0) REVERT: A 402 ASP cc_start: 0.3278 (m-30) cc_final: 0.2558 (p0) outliers start: 62 outliers final: 40 residues processed: 166 average time/residue: 0.1865 time to fit residues: 46.1511 Evaluate side-chains 149 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10426 Z= 0.193 Angle : 0.554 6.008 14158 Z= 0.293 Chirality : 0.040 0.145 1660 Planarity : 0.004 0.061 1720 Dihedral : 10.398 89.756 1486 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 6.39 % Allowed : 33.24 % Favored : 60.37 % 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: -1.79 (0.24), residues: 1240 helix: -0.81 (0.19), residues: 668 sheet: -1.31 (0.52), residues: 112 loop : -1.50 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.004 0.001 HIS A 416 PHE 0.016 0.001 PHE A 415 TYR 0.009 0.001 TYR A 228 ARG 0.004 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 112 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 206 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6447 (tttm) REVERT: C 238 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7377 (m) REVERT: C 388 LEU cc_start: 0.7092 (tp) cc_final: 0.6851 (mp) REVERT: C 402 ASP cc_start: 0.3333 (m-30) cc_final: 0.2595 (p0) REVERT: A 206 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6484 (tttm) REVERT: A 238 CYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7377 (m) REVERT: A 388 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6825 (mp) REVERT: A 402 ASP cc_start: 0.3274 (m-30) cc_final: 0.2602 (p0) outliers start: 69 outliers final: 47 residues processed: 174 average time/residue: 0.1899 time to fit residues: 49.7194 Evaluate side-chains 158 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 106 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.0670 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 0.0970 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10426 Z= 0.147 Angle : 0.529 8.274 14158 Z= 0.277 Chirality : 0.039 0.156 1660 Planarity : 0.003 0.032 1720 Dihedral : 10.302 89.980 1486 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.46 % Allowed : 34.35 % Favored : 60.19 % 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: -1.57 (0.24), residues: 1240 helix: -0.59 (0.20), residues: 670 sheet: -1.30 (0.51), residues: 112 loop : -1.46 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 95 HIS 0.004 0.001 HIS C 416 PHE 0.019 0.001 PHE C 415 TYR 0.009 0.001 TYR C 474 ARG 0.004 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 238 CYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7357 (m) REVERT: C 388 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6839 (mp) REVERT: C 402 ASP cc_start: 0.3244 (m-30) cc_final: 0.2693 (p0) REVERT: A 238 CYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7303 (m) REVERT: A 402 ASP cc_start: 0.3232 (m-30) cc_final: 0.2727 (p0) outliers start: 59 outliers final: 45 residues processed: 168 average time/residue: 0.1801 time to fit residues: 45.0267 Evaluate side-chains 160 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 ASN C 747 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10426 Z= 0.174 Angle : 0.553 7.328 14158 Z= 0.286 Chirality : 0.040 0.160 1660 Planarity : 0.004 0.034 1720 Dihedral : 10.257 89.679 1486 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 6.39 % Allowed : 33.33 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.24), residues: 1240 helix: -0.58 (0.20), residues: 674 sheet: -1.35 (0.51), residues: 112 loop : -1.47 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.003 0.001 HIS A 416 PHE 0.043 0.002 PHE A 87 TYR 0.010 0.001 TYR A 474 ARG 0.002 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 113 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 CYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7353 (m) REVERT: C 388 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6848 (mp) REVERT: C 402 ASP cc_start: 0.3402 (m-30) cc_final: 0.2879 (p0) REVERT: C 423 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6302 (mp0) REVERT: A 238 CYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7366 (m) REVERT: A 388 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6744 (mp) REVERT: A 402 ASP cc_start: 0.3258 (m-30) cc_final: 0.2784 (p0) outliers start: 69 outliers final: 55 residues processed: 168 average time/residue: 0.1589 time to fit residues: 41.8466 Evaluate side-chains 165 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 106 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.0170 chunk 82 optimal weight: 0.0040 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.3230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10426 Z= 0.132 Angle : 0.540 7.361 14158 Z= 0.274 Chirality : 0.039 0.172 1660 Planarity : 0.003 0.027 1720 Dihedral : 10.219 89.787 1486 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.81 % Allowed : 34.81 % Favored : 60.37 % 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: -1.37 (0.24), residues: 1240 helix: -0.42 (0.20), residues: 676 sheet: -1.35 (0.51), residues: 112 loop : -1.35 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 95 HIS 0.004 0.001 HIS A 416 PHE 0.050 0.002 PHE A 87 TYR 0.010 0.001 TYR A 474 ARG 0.002 0.000 ARG C 745 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 122 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 ASP cc_start: 0.3350 (m-30) cc_final: 0.2982 (p0) REVERT: C 423 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6257 (mp0) REVERT: A 259 VAL cc_start: 0.6000 (OUTLIER) cc_final: 0.5759 (t) REVERT: A 402 ASP cc_start: 0.3384 (m-30) cc_final: 0.3023 (p0) REVERT: A 423 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6258 (mp0) outliers start: 52 outliers final: 46 residues processed: 163 average time/residue: 0.2086 time to fit residues: 50.4684 Evaluate side-chains 158 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 111 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 68 optimal weight: 0.2980 chunk 49 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 0.0000 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10426 Z= 0.138 Angle : 0.531 7.298 14158 Z= 0.273 Chirality : 0.039 0.165 1660 Planarity : 0.003 0.027 1720 Dihedral : 10.175 89.754 1486 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.81 % Allowed : 34.91 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.24), residues: 1240 helix: -0.29 (0.20), residues: 674 sheet: -1.33 (0.50), residues: 112 loop : -1.34 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.003 0.000 HIS C 416 PHE 0.047 0.001 PHE A 87 TYR 0.011 0.001 TYR C 474 ARG 0.002 0.000 ARG C 745 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 114 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 ASP cc_start: 0.3348 (m-30) cc_final: 0.3113 (p0) REVERT: C 423 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6173 (mp0) REVERT: A 388 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6823 (mp) REVERT: A 402 ASP cc_start: 0.3287 (m-30) cc_final: 0.3039 (p0) REVERT: A 423 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6268 (mp0) outliers start: 52 outliers final: 44 residues processed: 155 average time/residue: 0.2185 time to fit residues: 49.5228 Evaluate side-chains 156 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 0.0060 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10426 Z= 0.131 Angle : 0.525 7.397 14158 Z= 0.270 Chirality : 0.039 0.169 1660 Planarity : 0.003 0.026 1720 Dihedral : 10.131 89.785 1486 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.26 % Allowed : 35.28 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1240 helix: -0.24 (0.21), residues: 680 sheet: -1.23 (0.49), residues: 114 loop : -1.39 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 95 HIS 0.003 0.000 HIS A 416 PHE 0.054 0.001 PHE A 87 TYR 0.010 0.001 TYR C 474 ARG 0.005 0.000 ARG A 438 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 118 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 423 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6160 (mp0) REVERT: A 423 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6154 (mp0) outliers start: 46 outliers final: 46 residues processed: 155 average time/residue: 0.1740 time to fit residues: 41.5302 Evaluate side-chains 156 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** 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 = 0.4429 r_free = 0.4429 target = 0.170966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.149120 restraints weight = 19382.100| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.13 r_work: 0.4026 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10426 Z= 0.147 Angle : 0.542 9.536 14158 Z= 0.279 Chirality : 0.040 0.181 1660 Planarity : 0.003 0.027 1720 Dihedral : 10.117 89.653 1486 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.26 % Allowed : 35.28 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1240 helix: -0.24 (0.21), residues: 680 sheet: -1.20 (0.50), residues: 114 loop : -1.39 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.003 0.001 HIS C 225 PHE 0.054 0.001 PHE A 87 TYR 0.011 0.001 TYR A 474 ARG 0.003 0.000 ARG A 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2363.99 seconds wall clock time: 42 minutes 54.04 seconds (2574.04 seconds total)