Starting phenix.real_space_refine on Wed Mar 20 17:50:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tet_25852/03_2024/7tet_25852.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tet_25852/03_2024/7tet_25852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tet_25852/03_2024/7tet_25852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tet_25852/03_2024/7tet_25852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tet_25852/03_2024/7tet_25852.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tet_25852/03_2024/7tet_25852.pdb" } resolution = 4.45 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= 0.044 sd= 0.420 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 172 5.16 5 C 17941 2.51 5 N 4707 2.21 5 O 5268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28088 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6194 Classifications: {'peptide': 786} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 753} Chain breaks: 5 Chain: "B" Number of atoms: 6079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6079 Classifications: {'peptide': 769} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 740} Chain breaks: 5 Chain: "C" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6194 Classifications: {'peptide': 786} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 753} Chain breaks: 5 Chain: "D" Number of atoms: 6085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6085 Classifications: {'peptide': 770} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 741} Chain breaks: 4 Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 110} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "M" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 110} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Time building chain proxies: 13.82, per 1000 atoms: 0.49 Number of scatterers: 28088 At special positions: 0 Unit cell: (141.11, 205.5, 182.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 172 16.00 O 5268 8.00 N 4707 7.00 C 17941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 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: 10.55 Conformation dependent library (CDL) restraints added in 4.8 seconds 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6626 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 46 sheets defined 38.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.500A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.887A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.623A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.716A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.507A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 4.357A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.926A pdb=" N ASP A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 582 through 602 removed outlier: 3.981A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 removed outlier: 4.076A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 677 removed outlier: 3.715A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.980A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 745 removed outlier: 3.929A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.077A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 802 Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.735A pdb=" N ALA A 835 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 836 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET A 839 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 840 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 841 " --> pdb=" O PHE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'B' and resid 46 through 54 removed outlier: 4.393A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.725A pdb=" N HIS B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.541A pdb=" N ILE B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.744A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.528A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.766A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 removed outlier: 3.846A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 282 through 308 removed outlier: 3.831A pdb=" N ASP B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 289 " --> pdb=" O TRP B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.521A pdb=" N ALA B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.687A pdb=" N GLN B 331 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 459 through 472 removed outlier: 4.168A pdb=" N ASP B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.609A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 519 No H-bonds generated for 'chain 'B' and resid 518 through 519' Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 551 through 576 removed outlier: 3.709A pdb=" N CYS B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 558 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 608 removed outlier: 3.531A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 626 through 655 removed outlier: 3.640A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 removed outlier: 4.082A pdb=" N ASP B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.874A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.932A pdb=" N ASN B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 removed outlier: 3.519A pdb=" N ALA B 717 " --> pdb=" O GLY B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 785 removed outlier: 3.662A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.514A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 removed outlier: 3.825A pdb=" N ALA B 819 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 820 " --> pdb=" O ASN B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 843 Processing helix chain 'C' and resid 35 through 49 removed outlier: 3.500A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.886A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.622A pdb=" N GLU C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.716A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.507A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 removed outlier: 4.356A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 491 removed outlier: 3.926A pdb=" N ASP C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 483 " --> pdb=" O PHE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 582 through 602 removed outlier: 3.980A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 4.075A pdb=" N PHE C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 677 removed outlier: 3.716A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.980A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 745 removed outlier: 3.928A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.078A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 802 Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 832 through 842 removed outlier: 3.736A pdb=" N ALA C 835 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 836 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET C 839 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 840 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 841 " --> pdb=" O PHE C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 862 Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.407A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.722A pdb=" N HIS D 60 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.514A pdb=" N ILE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.723A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.563A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 4.715A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.832A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 282 through 308 removed outlier: 3.881A pdb=" N ASP D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 289 " --> pdb=" O TRP D 285 " (cutoff:3.500A) Proline residue: D 290 - end of helix removed outlier: 3.500A pdb=" N ALA D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.702A pdb=" N GLN D 331 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 459 through 472 removed outlier: 4.150A pdb=" N ASP D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.602A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 576 removed outlier: 4.223A pdb=" N MET D 561 " --> pdb=" O CYS D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 608 removed outlier: 3.558A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 614 Processing helix chain 'D' and resid 626 through 655 removed outlier: 3.638A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 667 removed outlier: 3.609A pdb=" N LEU D 666 " --> pdb=" O GLN D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 4.177A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 704 Processing helix chain 'D' and resid 706 through 710 removed outlier: 3.936A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.520A pdb=" N ALA D 717 " --> pdb=" O GLY D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 785 removed outlier: 3.713A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.512A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 821 removed outlier: 3.800A pdb=" N ALA D 819 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 820 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 844 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.628A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.627A pdb=" N ASP M 90 " --> pdb=" O LYS M 87 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.632A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 240 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.306A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.514A pdb=" N HIS A 498 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.910A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA8, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AA9, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 73 removed outlier: 6.143A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 204 removed outlier: 3.640A pdb=" N SER B 170 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AB4, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.910A pdb=" N VAL B 342 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 377 through 379 Processing sheet with id=AB6, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AB7, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB9, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.125A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 534 through 537 Processing sheet with id=AC2, first strand: chain 'C' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.631A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE C 240 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.307A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 420 through 423 removed outlier: 3.513A pdb=" N HIS C 498 " --> pdb=" O ILE C 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 508 through 511 removed outlier: 3.909A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 533 through 535 Processing sheet with id=AC9, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD1, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD2, first strand: chain 'D' and resid 66 through 73 removed outlier: 6.167A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 201 through 204 removed outlier: 3.643A pdb=" N SER D 170 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 278 through 280 Processing sheet with id=AD5, first strand: chain 'D' and resid 341 through 344 removed outlier: 3.871A pdb=" N VAL D 342 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 377 through 379 Processing sheet with id=AD7, first strand: chain 'D' and resid 475 through 480 Processing sheet with id=AD8, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD9, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AE1, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.085A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 534 through 537 Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 8 removed outlier: 5.382A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.720A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.549A pdb=" N VAL L 13 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 4 through 8 removed outlier: 5.382A pdb=" N GLY M 16 " --> pdb=" O SER M 85 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP M 73 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.720A pdb=" N GLY M 10 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN M 57 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AF1, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.549A pdb=" N VAL N 13 " --> pdb=" O GLU N 109 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP N 39 " --> pdb=" O LEU N 51 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 2961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.03 Time building geometry restraints manager: 11.50 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: 8941 1.34 - 1.46: 6395 1.46 - 1.58: 13067 1.58 - 1.70: 2 1.70 - 1.82: 294 Bond restraints: 28699 Sorted by residual: bond pdb=" CB GLU C 683 " pdb=" CG GLU C 683 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.97e+00 bond pdb=" CB GLU A 683 " pdb=" CG GLU A 683 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.97e+00 bond pdb=" CG LYS B 185 " pdb=" CD LYS B 185 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.56e+00 bond pdb=" CB SER D 645 " pdb=" OG SER D 645 " ideal model delta sigma weight residual 1.417 1.380 0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C THR A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 ... (remaining 28694 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.33: 460 104.33 - 111.88: 12933 111.88 - 119.42: 10873 119.42 - 126.97: 14206 126.97 - 134.51: 379 Bond angle restraints: 38851 Sorted by residual: angle pdb=" N ILE D 800 " pdb=" CA ILE D 800 " pdb=" C ILE D 800 " ideal model delta sigma weight residual 111.48 104.08 7.40 9.40e-01 1.13e+00 6.20e+01 angle pdb=" C ASP M 102 " pdb=" N GLY M 103 " pdb=" CA GLY M 103 " ideal model delta sigma weight residual 121.70 132.74 -11.04 1.80e+00 3.09e-01 3.76e+01 angle pdb=" C ASP H 102 " pdb=" N GLY H 103 " pdb=" CA GLY H 103 " ideal model delta sigma weight residual 121.70 132.71 -11.01 1.80e+00 3.09e-01 3.74e+01 angle pdb=" C LYS B 768 " pdb=" N ASP B 769 " pdb=" CA ASP B 769 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" N ASN D 803 " pdb=" CA ASN D 803 " pdb=" C ASN D 803 " ideal model delta sigma weight residual 110.80 121.34 -10.54 2.13e+00 2.20e-01 2.45e+01 ... (remaining 38846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 15370 18.10 - 36.20: 1459 36.20 - 54.30: 236 54.30 - 72.39: 56 72.39 - 90.49: 18 Dihedral angle restraints: 17139 sinusoidal: 6833 harmonic: 10306 Sorted by residual: dihedral pdb=" CA HIS D 802 " pdb=" C HIS D 802 " pdb=" N ASN D 803 " pdb=" CA ASN D 803 " ideal model delta harmonic sigma weight residual -180.00 -120.98 -59.02 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA HIS B 802 " pdb=" C HIS B 802 " pdb=" N ASN B 803 " pdb=" CA ASN B 803 " ideal model delta harmonic sigma weight residual -180.00 -121.55 -58.45 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CB CYS A 441 " pdb=" SG CYS A 441 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual -86.00 -176.49 90.49 1 1.00e+01 1.00e-02 9.68e+01 ... (remaining 17136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3602 0.079 - 0.159: 641 0.159 - 0.238: 68 0.238 - 0.317: 17 0.317 - 0.397: 5 Chirality restraints: 4333 Sorted by residual: chirality pdb=" CB VAL C 270 " pdb=" CA VAL C 270 " pdb=" CG1 VAL C 270 " pdb=" CG2 VAL C 270 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB VAL A 270 " pdb=" CA VAL A 270 " pdb=" CG1 VAL A 270 " pdb=" CG2 VAL A 270 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE D 751 " pdb=" CA ILE D 751 " pdb=" CG1 ILE D 751 " pdb=" CG2 ILE D 751 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 4330 not shown) Planarity restraints: 4936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 679 " -0.063 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO D 680 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 680 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 680 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 47 " 0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO N 48 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO N 48 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO N 48 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 47 " 0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO L 48 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO L 48 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 48 " 0.053 5.00e-02 4.00e+02 ... (remaining 4933 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4637 2.76 - 3.29: 26893 3.29 - 3.83: 49279 3.83 - 4.36: 55956 4.36 - 4.90: 89481 Nonbonded interactions: 226246 Sorted by model distance: nonbonded pdb=" OH TYR C 114 " pdb=" O CYS C 329 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR A 114 " pdb=" O CYS A 329 " model vdw 2.225 2.440 nonbonded pdb=" O SER B 320 " pdb=" OG1 THR B 324 " model vdw 2.229 2.440 nonbonded pdb=" O SER D 320 " pdb=" OG1 THR D 324 " model vdw 2.234 2.440 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.236 2.440 ... (remaining 226241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 34 through 519 or resid 521 through 845)) } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.040 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 71.660 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 28699 Z= 0.342 Angle : 1.033 15.948 38851 Z= 0.579 Chirality : 0.062 0.397 4333 Planarity : 0.008 0.096 4936 Dihedral : 14.450 82.866 10471 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.63 % Favored : 88.91 % Rotamer: Outliers : 0.78 % Allowed : 8.47 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 4.48 % Twisted General : 1.09 % 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: -4.42 (0.12), residues: 3509 helix: -3.09 (0.10), residues: 1156 sheet: -2.53 (0.20), residues: 534 loop : -2.96 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 657 HIS 0.019 0.003 HIS D 703 PHE 0.037 0.003 PHE B 525 TYR 0.042 0.003 TYR D 823 ARG 0.010 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.9103 (m170) cc_final: 0.8622 (t70) REVERT: A 155 MET cc_start: 0.9267 (mpp) cc_final: 0.8683 (mmp) REVERT: A 261 MET cc_start: 0.9450 (mmm) cc_final: 0.9081 (mmm) REVERT: A 576 MET cc_start: 0.9220 (mtp) cc_final: 0.8487 (tmm) REVERT: A 662 MET cc_start: 0.9742 (ppp) cc_final: 0.9295 (ppp) REVERT: A 751 ILE cc_start: 0.9848 (mt) cc_final: 0.9601 (tp) REVERT: C 134 HIS cc_start: 0.9121 (m170) cc_final: 0.8539 (t70) REVERT: C 261 MET cc_start: 0.9462 (mmm) cc_final: 0.9110 (mmm) REVERT: C 576 MET cc_start: 0.9197 (mtp) cc_final: 0.8464 (tmm) REVERT: C 662 MET cc_start: 0.9741 (ppp) cc_final: 0.9294 (ppp) REVERT: C 751 ILE cc_start: 0.9841 (mt) cc_final: 0.9591 (tp) REVERT: D 721 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9388 (pt) REVERT: H 106 MET cc_start: 0.7779 (mpp) cc_final: 0.7458 (mpp) REVERT: N 58 LEU cc_start: 0.9539 (pp) cc_final: 0.9295 (mp) outliers start: 24 outliers final: 3 residues processed: 212 average time/residue: 0.3606 time to fit residues: 126.2272 Evaluate side-chains 160 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 5.9990 chunk 267 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 320 optimal weight: 40.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 59 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 362 ASN A 378 GLN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 492 GLN A 515 ASN A 717 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS B 649 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN B 812 GLN C 47 ASN C 59 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 362 ASN C 378 GLN C 425 HIS C 492 GLN C 515 ASN C 717 GLN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 HIS D 192 ASN ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS D 782 GLN D 812 GLN H 82 GLN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN N 94 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28699 Z= 0.204 Angle : 0.665 7.961 38851 Z= 0.359 Chirality : 0.044 0.315 4333 Planarity : 0.005 0.091 4936 Dihedral : 7.082 51.640 3836 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.60 % Favored : 90.17 % Rotamer: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 1.49 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.13), residues: 3509 helix: -1.21 (0.13), residues: 1169 sheet: -2.19 (0.20), residues: 596 loop : -2.72 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 813 HIS 0.006 0.001 HIS D 703 PHE 0.031 0.001 PHE D 525 TYR 0.018 0.001 TYR D 823 ARG 0.006 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.9046 (m170) cc_final: 0.8654 (t70) REVERT: A 523 MET cc_start: 0.9643 (mmm) cc_final: 0.8823 (mtp) REVERT: A 576 MET cc_start: 0.9221 (mtp) cc_final: 0.8487 (tmm) REVERT: A 751 ILE cc_start: 0.9814 (mt) cc_final: 0.9567 (tp) REVERT: B 497 MET cc_start: 0.9398 (mtm) cc_final: 0.9131 (mpp) REVERT: C 134 HIS cc_start: 0.9076 (m170) cc_final: 0.8529 (t70) REVERT: C 523 MET cc_start: 0.9651 (mmm) cc_final: 0.8774 (mtp) REVERT: C 576 MET cc_start: 0.9201 (mtp) cc_final: 0.8465 (tmm) REVERT: D 497 MET cc_start: 0.9464 (mtm) cc_final: 0.9172 (mpp) REVERT: H 33 TYR cc_start: 0.8583 (t80) cc_final: 0.8309 (t80) REVERT: H 106 MET cc_start: 0.7705 (mpp) cc_final: 0.7451 (mpp) REVERT: N 51 LEU cc_start: 0.9656 (pt) cc_final: 0.9287 (pt) outliers start: 4 outliers final: 0 residues processed: 171 average time/residue: 0.3740 time to fit residues: 106.2513 Evaluate side-chains 149 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 321 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 318 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 257 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS B 118 GLN ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN B 802 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 323 ASN D 649 ASN ** D 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN H 111 GLN L 80 HIS ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28699 Z= 0.190 Angle : 0.628 12.131 38851 Z= 0.338 Chirality : 0.044 0.244 4333 Planarity : 0.004 0.088 4936 Dihedral : 6.661 42.113 3836 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.80 % Favored : 90.03 % Rotamer: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -2.59 (0.14), residues: 3509 helix: -0.36 (0.14), residues: 1191 sheet: -1.93 (0.21), residues: 584 loop : -2.68 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.006 0.001 HIS L 80 PHE 0.042 0.002 PHE D 144 TYR 0.044 0.001 TYR H 33 ARG 0.005 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.9056 (m170) cc_final: 0.8675 (t70) REVERT: A 415 MET cc_start: 0.7975 (tpp) cc_final: 0.7529 (tpp) REVERT: A 523 MET cc_start: 0.9507 (mmm) cc_final: 0.8821 (mtp) REVERT: A 576 MET cc_start: 0.9254 (mtp) cc_final: 0.8525 (tmm) REVERT: B 497 MET cc_start: 0.9425 (mtm) cc_final: 0.9122 (mpp) REVERT: B 654 MET cc_start: 0.9502 (mmp) cc_final: 0.9162 (mmp) REVERT: C 134 HIS cc_start: 0.9127 (m170) cc_final: 0.8611 (t70) REVERT: C 415 MET cc_start: 0.8055 (tpp) cc_final: 0.7719 (tpp) REVERT: C 523 MET cc_start: 0.9511 (mmm) cc_final: 0.8721 (mtp) REVERT: C 576 MET cc_start: 0.9253 (mtp) cc_final: 0.8499 (tmm) REVERT: D 497 MET cc_start: 0.9480 (mtm) cc_final: 0.9198 (mpp) REVERT: D 654 MET cc_start: 0.9489 (mmp) cc_final: 0.9115 (mmp) REVERT: H 106 MET cc_start: 0.7521 (mpp) cc_final: 0.7170 (mpp) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.3702 time to fit residues: 102.0555 Evaluate side-chains 149 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 40.0000 chunk 241 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 chunk 341 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN B 331 GLN B 694 ASN B 697 ASN B 710 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS D 60 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 697 ASN D 710 ASN D 802 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 28699 Z= 0.378 Angle : 0.789 9.818 38851 Z= 0.420 Chirality : 0.045 0.379 4333 Planarity : 0.005 0.086 4936 Dihedral : 6.928 44.274 3836 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.26 % Favored : 88.52 % Rotamer: Outliers : 0.10 % Allowed : 4.22 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -2.56 (0.14), residues: 3509 helix: -0.23 (0.14), residues: 1187 sheet: -1.98 (0.22), residues: 540 loop : -2.71 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 96 HIS 0.009 0.002 HIS N 80 PHE 0.043 0.002 PHE D 525 TYR 0.047 0.002 TYR M 33 ARG 0.008 0.001 ARG M 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.8121 (tpp) cc_final: 0.7773 (tpp) REVERT: A 523 MET cc_start: 0.9604 (mmm) cc_final: 0.9002 (mtp) REVERT: A 576 MET cc_start: 0.9274 (mtp) cc_final: 0.8563 (tmm) REVERT: A 834 MET cc_start: 0.9221 (mpp) cc_final: 0.8885 (mpp) REVERT: B 497 MET cc_start: 0.9465 (mtm) cc_final: 0.9165 (mpp) REVERT: B 508 MET cc_start: 0.9649 (mmm) cc_final: 0.9319 (mmm) REVERT: B 565 MET cc_start: 0.9671 (mtm) cc_final: 0.9419 (mtt) REVERT: B 654 MET cc_start: 0.9512 (mmp) cc_final: 0.9121 (mmm) REVERT: C 415 MET cc_start: 0.8095 (tpp) cc_final: 0.7798 (tpp) REVERT: C 523 MET cc_start: 0.9507 (mmm) cc_final: 0.8720 (mtp) REVERT: C 576 MET cc_start: 0.9260 (mtp) cc_final: 0.8528 (tmm) REVERT: C 834 MET cc_start: 0.9212 (mpp) cc_final: 0.8939 (mpp) REVERT: D 497 MET cc_start: 0.9508 (mtm) cc_final: 0.9209 (mpp) REVERT: D 562 MET cc_start: 0.9702 (mmp) cc_final: 0.9495 (mmt) REVERT: D 654 MET cc_start: 0.9512 (mmp) cc_final: 0.9112 (mmm) outliers start: 3 outliers final: 0 residues processed: 163 average time/residue: 0.3844 time to fit residues: 104.8207 Evaluate side-chains 147 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 40.0000 chunk 140 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 174 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** D 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28699 Z= 0.290 Angle : 0.706 12.375 38851 Z= 0.377 Chirality : 0.044 0.278 4333 Planarity : 0.005 0.097 4936 Dihedral : 6.824 41.502 3836 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.77 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -2.42 (0.14), residues: 3509 helix: 0.00 (0.15), residues: 1189 sheet: -1.94 (0.22), residues: 516 loop : -2.71 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 109 HIS 0.007 0.001 HIS L 94 PHE 0.045 0.002 PHE B 525 TYR 0.034 0.002 TYR M 33 ARG 0.005 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.8188 (tpp) cc_final: 0.7815 (tpp) REVERT: A 523 MET cc_start: 0.9793 (mmm) cc_final: 0.8964 (mtp) REVERT: A 576 MET cc_start: 0.9314 (mtp) cc_final: 0.8659 (tmm) REVERT: A 834 MET cc_start: 0.9316 (mpp) cc_final: 0.9076 (mpp) REVERT: B 497 MET cc_start: 0.9483 (mtm) cc_final: 0.9206 (mpp) REVERT: B 508 MET cc_start: 0.9505 (mmm) cc_final: 0.9250 (mmm) REVERT: B 654 MET cc_start: 0.9522 (mmp) cc_final: 0.9108 (mmm) REVERT: C 415 MET cc_start: 0.8200 (tpp) cc_final: 0.7857 (tpp) REVERT: C 523 MET cc_start: 0.9533 (mmm) cc_final: 0.8695 (mmm) REVERT: C 576 MET cc_start: 0.9259 (mtp) cc_final: 0.8558 (tmm) REVERT: C 834 MET cc_start: 0.9324 (mpp) cc_final: 0.9066 (mpp) REVERT: D 497 MET cc_start: 0.9520 (mtm) cc_final: 0.9262 (mpp) REVERT: D 654 MET cc_start: 0.9524 (mmp) cc_final: 0.9095 (mmm) REVERT: D 789 MET cc_start: 0.9269 (pmm) cc_final: 0.9044 (pmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3910 time to fit residues: 101.3721 Evaluate side-chains 145 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS A 530 GLN A 745 ASN B 331 GLN B 710 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28699 Z= 0.282 Angle : 0.699 8.910 38851 Z= 0.374 Chirality : 0.044 0.241 4333 Planarity : 0.005 0.083 4936 Dihedral : 6.782 40.707 3836 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.80 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -2.34 (0.14), residues: 3509 helix: 0.08 (0.15), residues: 1196 sheet: -1.82 (0.23), residues: 484 loop : -2.71 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 268 HIS 0.007 0.001 HIS L 94 PHE 0.053 0.002 PHE B 144 TYR 0.030 0.002 TYR M 33 ARG 0.006 0.001 ARG C 692 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.8510 (tpp) cc_final: 0.8082 (tpp) REVERT: A 523 MET cc_start: 0.9788 (mmm) cc_final: 0.8982 (mtp) REVERT: A 576 MET cc_start: 0.9265 (mtp) cc_final: 0.8594 (tmm) REVERT: A 834 MET cc_start: 0.9346 (mpp) cc_final: 0.9093 (mpp) REVERT: B 497 MET cc_start: 0.9500 (mtm) cc_final: 0.9232 (mpp) REVERT: B 654 MET cc_start: 0.9526 (mmp) cc_final: 0.9105 (mmm) REVERT: C 415 MET cc_start: 0.8445 (tpp) cc_final: 0.8088 (tpp) REVERT: C 523 MET cc_start: 0.9515 (mmm) cc_final: 0.8608 (mmm) REVERT: C 576 MET cc_start: 0.9243 (mtp) cc_final: 0.8551 (tmm) REVERT: C 834 MET cc_start: 0.9363 (mpp) cc_final: 0.9125 (mpp) REVERT: D 497 MET cc_start: 0.9550 (mtm) cc_final: 0.9222 (mpp) REVERT: D 508 MET cc_start: 0.7738 (mmp) cc_final: 0.7520 (mmm) REVERT: D 654 MET cc_start: 0.9529 (mmp) cc_final: 0.9094 (mmm) REVERT: M 106 MET cc_start: 0.7504 (mtp) cc_final: 0.6674 (mmp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3962 time to fit residues: 101.1774 Evaluate side-chains 140 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 287 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 340 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28699 Z= 0.246 Angle : 0.673 7.924 38851 Z= 0.358 Chirality : 0.044 0.270 4333 Planarity : 0.004 0.087 4936 Dihedral : 6.648 39.806 3836 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.26 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.14), residues: 3509 helix: 0.23 (0.15), residues: 1201 sheet: -1.75 (0.23), residues: 482 loop : -2.73 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 610 HIS 0.006 0.001 HIS L 94 PHE 0.047 0.002 PHE D 525 TYR 0.026 0.002 TYR M 33 ARG 0.005 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.9004 (mmt) cc_final: 0.8151 (mmt) REVERT: A 415 MET cc_start: 0.8596 (tpp) cc_final: 0.8236 (tpp) REVERT: A 523 MET cc_start: 0.9798 (mmm) cc_final: 0.9122 (mtp) REVERT: A 576 MET cc_start: 0.9381 (mtp) cc_final: 0.8613 (tmm) REVERT: A 834 MET cc_start: 0.9348 (mpp) cc_final: 0.9138 (mpp) REVERT: B 497 MET cc_start: 0.9506 (mtm) cc_final: 0.9200 (mpp) REVERT: B 654 MET cc_start: 0.9557 (mmp) cc_final: 0.9217 (mmm) REVERT: C 261 MET cc_start: 0.8945 (mmt) cc_final: 0.8181 (mmm) REVERT: C 415 MET cc_start: 0.8526 (tpp) cc_final: 0.8168 (tpp) REVERT: C 523 MET cc_start: 0.9524 (mmm) cc_final: 0.8611 (mmm) REVERT: C 576 MET cc_start: 0.9379 (mtp) cc_final: 0.8525 (tmm) REVERT: D 497 MET cc_start: 0.9570 (mtm) cc_final: 0.9242 (mpp) REVERT: D 537 MET cc_start: 0.9032 (tpt) cc_final: 0.8802 (tpp) REVERT: D 654 MET cc_start: 0.9572 (mmp) cc_final: 0.9211 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3769 time to fit residues: 96.2105 Evaluate side-chains 139 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN D 331 GLN D 710 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 28699 Z= 0.264 Angle : 0.697 14.530 38851 Z= 0.369 Chirality : 0.044 0.292 4333 Planarity : 0.005 0.164 4936 Dihedral : 6.694 39.560 3836 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.80 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3509 helix: 0.24 (0.15), residues: 1205 sheet: -1.84 (0.23), residues: 496 loop : -2.73 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 610 HIS 0.006 0.001 HIS L 94 PHE 0.050 0.002 PHE B 525 TYR 0.045 0.002 TYR H 33 ARG 0.017 0.001 ARG N 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8897 (mmt) cc_final: 0.8006 (mmt) REVERT: A 415 MET cc_start: 0.8648 (tpp) cc_final: 0.8218 (tpp) REVERT: A 523 MET cc_start: 0.9796 (mmm) cc_final: 0.9187 (mtp) REVERT: A 576 MET cc_start: 0.9384 (mtp) cc_final: 0.8558 (tmm) REVERT: B 497 MET cc_start: 0.9508 (mtm) cc_final: 0.9163 (mpp) REVERT: B 537 MET cc_start: 0.8998 (tpt) cc_final: 0.8699 (tpp) REVERT: B 562 MET cc_start: 0.9711 (mpp) cc_final: 0.9392 (mmt) REVERT: B 654 MET cc_start: 0.9557 (mmp) cc_final: 0.9208 (mmm) REVERT: C 261 MET cc_start: 0.8899 (mmt) cc_final: 0.8018 (mmt) REVERT: C 375 MET cc_start: 0.9000 (tpt) cc_final: 0.8432 (mmm) REVERT: C 415 MET cc_start: 0.8588 (tpp) cc_final: 0.8230 (tpp) REVERT: C 523 MET cc_start: 0.9528 (mmm) cc_final: 0.8722 (mmm) REVERT: C 576 MET cc_start: 0.9375 (mtp) cc_final: 0.8529 (tmm) REVERT: C 783 MET cc_start: 0.9057 (ttp) cc_final: 0.8851 (tpt) REVERT: C 834 MET cc_start: 0.9409 (mpp) cc_final: 0.9184 (mpp) REVERT: D 497 MET cc_start: 0.9586 (mtm) cc_final: 0.9350 (mpp) REVERT: D 537 MET cc_start: 0.9070 (tpt) cc_final: 0.8833 (tpp) REVERT: D 654 MET cc_start: 0.9578 (mmp) cc_final: 0.9213 (mmm) REVERT: M 106 MET cc_start: 0.7051 (mtm) cc_final: 0.6572 (mmp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3908 time to fit residues: 101.3553 Evaluate side-chains 142 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 40.0000 chunk 325 optimal weight: 0.0770 chunk 297 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 286 optimal weight: 0.0020 chunk 299 optimal weight: 20.0000 chunk 315 optimal weight: 7.9990 overall best weight: 4.0152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 323 ASN D 331 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 HIS ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28699 Z= 0.218 Angle : 0.671 17.262 38851 Z= 0.353 Chirality : 0.044 0.261 4333 Planarity : 0.005 0.141 4936 Dihedral : 6.580 38.943 3836 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.23 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.14), residues: 3509 helix: 0.35 (0.15), residues: 1211 sheet: -1.90 (0.23), residues: 488 loop : -2.69 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 610 HIS 0.009 0.001 HIS L 94 PHE 0.040 0.002 PHE B 525 TYR 0.032 0.002 TYR H 33 ARG 0.010 0.001 ARG N 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8584 (mmp) cc_final: 0.8104 (tpt) REVERT: A 261 MET cc_start: 0.8955 (mmt) cc_final: 0.8053 (mmt) REVERT: A 415 MET cc_start: 0.8681 (tpp) cc_final: 0.8339 (tpp) REVERT: A 523 MET cc_start: 0.9792 (mmm) cc_final: 0.9179 (mtp) REVERT: A 576 MET cc_start: 0.9372 (mtp) cc_final: 0.8543 (tmm) REVERT: A 834 MET cc_start: 0.9448 (mpp) cc_final: 0.9218 (mpp) REVERT: B 497 MET cc_start: 0.9501 (mtm) cc_final: 0.9210 (mpp) REVERT: B 537 MET cc_start: 0.9062 (tpt) cc_final: 0.8829 (tpp) REVERT: B 654 MET cc_start: 0.9552 (mmp) cc_final: 0.9195 (mmm) REVERT: C 155 MET cc_start: 0.8717 (mmp) cc_final: 0.8343 (tpt) REVERT: C 261 MET cc_start: 0.9013 (mmt) cc_final: 0.8166 (mmt) REVERT: C 375 MET cc_start: 0.9199 (tpt) cc_final: 0.8790 (mmm) REVERT: C 415 MET cc_start: 0.8621 (tpp) cc_final: 0.8268 (tpp) REVERT: C 523 MET cc_start: 0.9557 (mmm) cc_final: 0.8810 (mmm) REVERT: C 576 MET cc_start: 0.9363 (mtp) cc_final: 0.8517 (tmm) REVERT: C 783 MET cc_start: 0.9052 (ttp) cc_final: 0.8840 (tpt) REVERT: C 834 MET cc_start: 0.9386 (mpp) cc_final: 0.9152 (mpp) REVERT: D 497 MET cc_start: 0.9602 (mtm) cc_final: 0.9361 (mpp) REVERT: D 537 MET cc_start: 0.9118 (tpt) cc_final: 0.8862 (tpp) REVERT: D 654 MET cc_start: 0.9573 (mmp) cc_final: 0.9194 (mmm) REVERT: M 106 MET cc_start: 0.7530 (mtm) cc_final: 0.7299 (mtp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3697 time to fit residues: 93.1975 Evaluate side-chains 138 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 0.5980 chunk 335 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 351 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 280 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 216 optimal weight: 0.1980 chunk 171 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28699 Z= 0.185 Angle : 0.660 18.941 38851 Z= 0.344 Chirality : 0.045 0.253 4333 Planarity : 0.005 0.129 4936 Dihedral : 6.395 38.127 3836 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.60 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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 (0.14), residues: 3509 helix: 0.52 (0.15), residues: 1212 sheet: -1.86 (0.22), residues: 505 loop : -2.60 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 166 HIS 0.006 0.001 HIS N 94 PHE 0.032 0.001 PHE B 525 TYR 0.038 0.001 TYR M 33 ARG 0.008 0.000 ARG N 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8684 (mmp) cc_final: 0.8209 (tpt) REVERT: A 261 MET cc_start: 0.8993 (mmt) cc_final: 0.8140 (mmt) REVERT: A 375 MET cc_start: 0.9181 (mmm) cc_final: 0.8369 (mmm) REVERT: A 415 MET cc_start: 0.8760 (tpp) cc_final: 0.8442 (tpp) REVERT: A 523 MET cc_start: 0.9797 (mmm) cc_final: 0.9210 (mtp) REVERT: A 576 MET cc_start: 0.9366 (mtp) cc_final: 0.8525 (tmm) REVERT: A 834 MET cc_start: 0.9387 (mpp) cc_final: 0.9116 (mpp) REVERT: B 497 MET cc_start: 0.9529 (mtm) cc_final: 0.9218 (mpp) REVERT: B 537 MET cc_start: 0.9030 (tpt) cc_final: 0.8771 (tpp) REVERT: B 654 MET cc_start: 0.9541 (mmp) cc_final: 0.9190 (mmp) REVERT: C 155 MET cc_start: 0.8754 (mmp) cc_final: 0.8340 (tpt) REVERT: C 261 MET cc_start: 0.8987 (mmt) cc_final: 0.8135 (mmt) REVERT: C 375 MET cc_start: 0.9319 (tpt) cc_final: 0.8806 (mmm) REVERT: C 415 MET cc_start: 0.8675 (tpp) cc_final: 0.8435 (tpp) REVERT: C 523 MET cc_start: 0.9565 (mmm) cc_final: 0.8856 (mmm) REVERT: C 576 MET cc_start: 0.9355 (mtp) cc_final: 0.8500 (tmm) REVERT: C 783 MET cc_start: 0.9045 (ttp) cc_final: 0.8798 (tpt) REVERT: C 834 MET cc_start: 0.9417 (mpp) cc_final: 0.9200 (mpp) REVERT: D 497 MET cc_start: 0.9606 (mtm) cc_final: 0.9361 (mpp) REVERT: D 537 MET cc_start: 0.9114 (tpt) cc_final: 0.8883 (tpp) REVERT: D 654 MET cc_start: 0.9570 (mmp) cc_final: 0.9188 (mmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3649 time to fit residues: 92.6596 Evaluate side-chains 140 residues out of total 3081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 41 optimal weight: 0.0070 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN D 331 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.027331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.022124 restraints weight = 492785.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.022754 restraints weight = 302140.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.023191 restraints weight = 212949.498| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28699 Z= 0.182 Angle : 0.640 10.932 38851 Z= 0.336 Chirality : 0.044 0.244 4333 Planarity : 0.005 0.118 4936 Dihedral : 6.283 37.227 3836 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.52 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -1.94 (0.14), residues: 3509 helix: 0.61 (0.15), residues: 1211 sheet: -1.82 (0.22), residues: 545 loop : -2.58 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 166 HIS 0.006 0.001 HIS N 42 PHE 0.029 0.001 PHE B 525 TYR 0.034 0.001 TYR M 33 ARG 0.006 0.000 ARG N 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.91 seconds wall clock time: 79 minutes 2.02 seconds (4742.02 seconds total)