Starting phenix.real_space_refine on Wed Feb 21 01:06:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1b_22623/02_2024/7k1b_22623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1b_22623/02_2024/7k1b_22623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1b_22623/02_2024/7k1b_22623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1b_22623/02_2024/7k1b_22623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1b_22623/02_2024/7k1b_22623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1b_22623/02_2024/7k1b_22623.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 185 5.16 5 C 18651 2.51 5 N 4987 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A TYR 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 744": "OD1" <-> "OD2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ASP 877": "OD1" <-> "OD2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ASP 1022": "OD1" <-> "OD2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A ARG 1155": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1328": "OE1" <-> "OE2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A ASP 1576": "OD1" <-> "OD2" Residue "A ASP 1602": "OD1" <-> "OD2" Residue "A GLU 1640": "OE1" <-> "OE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1708": "OE1" <-> "OE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A ARG 1727": "NH1" <-> "NH2" Residue "A ARG 1735": "NH1" <-> "NH2" Residue "A TYR 1739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1748": "OD1" <-> "OD2" Residue "A GLU 1776": "OE1" <-> "OE2" Residue "A PHE 1778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1787": "NH1" <-> "NH2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ASP 1849": "OD1" <-> "OD2" Residue "A PHE 1855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A PHE 1990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A GLU 2180": "OE1" <-> "OE2" Residue "A ARG 2214": "NH1" <-> "NH2" Residue "A ARG 2228": "NH1" <-> "NH2" Residue "A TYR 2253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A PHE 2260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A TYR 2316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A ARG 2427": "NH1" <-> "NH2" Residue "A ASP 2428": "OD1" <-> "OD2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A PHE 2840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2940": "NH1" <-> "NH2" Residue "A TYR 3040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3097": "OD1" <-> "OD2" Residue "A TYR 3102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3118": "OD1" <-> "OD2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A ARG 3247": "NH1" <-> "NH2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3344": "OE1" <-> "OE2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A TYR 3475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3507": "OD1" <-> "OD2" Residue "A GLU 3611": "OE1" <-> "OE2" Residue "A ARG 3612": "NH1" <-> "NH2" Residue "A ASP 3619": "OD1" <-> "OD2" Residue "A PHE 3628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3630": "NH1" <-> "NH2" Residue "A ASP 3641": "OD1" <-> "OD2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ASP 3661": "OD1" <-> "OD2" Residue "A GLU 3693": "OE1" <-> "OE2" Residue "A PHE 3694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A ASP 3723": "OD1" <-> "OD2" Residue "A ARG 3733": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3763": "NH1" <-> "NH2" Residue "A GLU 3807": "OE1" <-> "OE2" Residue "A ASP 3814": "OD1" <-> "OD2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A TYR 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A PHE 3897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A PHE 3942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A TYR 3981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4109": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 28343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3589, 28343 Classifications: {'peptide': 3589} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 146, 'TRANS': 3441} Chain breaks: 21 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 556 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 3, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 39, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 298 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 16.09, per 1000 atoms: 0.55 Number of scatterers: 29321 At special positions: 0 Unit cell: (124.12, 147.32, 183.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 185 16.00 P 46 15.00 O 5452 8.00 N 4987 7.00 C 18651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.60 Conformation dependent library (CDL) restraints added in 5.8 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 4 sheets defined 67.0% alpha, 1.2% beta 23 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 11.70 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 27 through 42 removed outlier: 3.592A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.516A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 96 removed outlier: 3.835A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.975A pdb=" N ALA A 127 " --> pdb=" O CYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.566A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 4.020A pdb=" N TYR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.957A pdb=" N GLU A 188 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.852A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.147A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.930A pdb=" N SER A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.865A pdb=" N LEU A 287 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP A 288 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 305 through 330 removed outlier: 4.275A pdb=" N LYS A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.110A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.950A pdb=" N VAL A 375 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 376 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 396 removed outlier: 4.995A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 removed outlier: 3.647A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.996A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.793A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.719A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 541 Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.656A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.662A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 658 removed outlier: 4.449A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.875A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.234A pdb=" N SER A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 758 removed outlier: 3.722A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.322A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 removed outlier: 4.118A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 847 through 862 removed outlier: 4.176A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.789A pdb=" N ASN A 869 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 883 Processing helix chain 'A' and resid 910 through 920 removed outlier: 4.291A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 944 removed outlier: 4.257A pdb=" N VAL A 928 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 947 No H-bonds generated for 'chain 'A' and resid 945 through 947' Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.905A pdb=" N LYS A 963 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 4.540A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1003 through 1018 removed outlier: 3.967A pdb=" N VAL A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1042 removed outlier: 3.573A pdb=" N ASP A1027 " --> pdb=" O SER A1023 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1067 removed outlier: 3.639A pdb=" N LEU A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1084 removed outlier: 4.275A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1114 Processing helix chain 'A' and resid 1122 through 1139 removed outlier: 3.601A pdb=" N ARG A1136 " --> pdb=" O ASP A1132 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 3.590A pdb=" N HIS A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1213 removed outlier: 3.663A pdb=" N LEU A1208 " --> pdb=" O PRO A1204 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1219 through 1226 Processing helix chain 'A' and resid 1241 through 1245 Processing helix chain 'A' and resid 1252 through 1273 removed outlier: 4.066A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A1270 " --> pdb=" O CYS A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1300 Processing helix chain 'A' and resid 1326 through 1336 removed outlier: 3.604A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1350 Processing helix chain 'A' and resid 1352 through 1356 removed outlier: 4.362A pdb=" N GLY A1355 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.239A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1407 Proline residue: A1396 - end of helix removed outlier: 3.679A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A1403 " --> pdb=" O CYS A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1431 removed outlier: 3.802A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1462 Processing helix chain 'A' and resid 1477 through 1490 Processing helix chain 'A' and resid 1505 through 1520 Processing helix chain 'A' and resid 1524 through 1532 removed outlier: 3.830A pdb=" N LEU A1528 " --> pdb=" O LEU A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1563 removed outlier: 3.947A pdb=" N TYR A1560 " --> pdb=" O GLY A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.837A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1585 removed outlier: 3.549A pdb=" N GLU A1581 " --> pdb=" O LEU A1577 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.749A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1610 No H-bonds generated for 'chain 'A' and resid 1608 through 1610' Processing helix chain 'A' and resid 1613 through 1624 Processing helix chain 'A' and resid 1625 through 1629 removed outlier: 3.552A pdb=" N LYS A1628 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A1629 " --> pdb=" O TRP A1626 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1625 through 1629' Processing helix chain 'A' and resid 1640 through 1655 Processing helix chain 'A' and resid 1667 through 1678 Processing helix chain 'A' and resid 1688 through 1700 removed outlier: 3.941A pdb=" N ALA A1692 " --> pdb=" O LEU A1688 " (cutoff:3.500A) Proline residue: A1697 - end of helix Processing helix chain 'A' and resid 1705 through 1722 removed outlier: 3.889A pdb=" N ALA A1720 " --> pdb=" O GLN A1716 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1751 removed outlier: 3.879A pdb=" N ASN A1737 " --> pdb=" O THR A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1757 through 1767 removed outlier: 3.901A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 3.966A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.534A pdb=" N GLN A1794 " --> pdb=" O SER A1790 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A1795 " --> pdb=" O CYS A1791 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A1796 " --> pdb=" O VAL A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.738A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1843 through 1848 removed outlier: 3.806A pdb=" N ALA A1847 " --> pdb=" O ILE A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 5.239A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A1883 " --> pdb=" O VAL A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1893 through 1900 removed outlier: 3.611A pdb=" N ASN A1897 " --> pdb=" O GLU A1893 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A1898 " --> pdb=" O SER A1894 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A1899 " --> pdb=" O LYS A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1922 removed outlier: 3.712A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE A1916 " --> pdb=" O THR A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1955 Processing helix chain 'A' and resid 1970 through 1974 Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 4.497A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2048 removed outlier: 4.110A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2126 through 2132 Processing helix chain 'A' and resid 2139 through 2151 removed outlier: 3.797A pdb=" N LEU A2149 " --> pdb=" O PHE A2145 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A2150 " --> pdb=" O LEU A2146 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.771A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2161 No H-bonds generated for 'chain 'A' and resid 2159 through 2161' Processing helix chain 'A' and resid 2165 through 2173 Processing helix chain 'A' and resid 2182 through 2194 Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 removed outlier: 3.910A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A2232 " --> pdb=" O ARG A2228 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N HIS A2233 " --> pdb=" O ALA A2229 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2282 Processing helix chain 'A' and resid 2295 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.517A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2354 removed outlier: 3.621A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2371 removed outlier: 3.676A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 3.887A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2385 Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.638A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 removed outlier: 3.589A pdb=" N LEU A2415 " --> pdb=" O LEU A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2425 removed outlier: 3.679A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2442 removed outlier: 3.641A pdb=" N GLN A2432 " --> pdb=" O ASP A2428 " (cutoff:3.500A) Processing helix chain 'A' and resid 2443 through 2446 Processing helix chain 'A' and resid 2447 through 2455 removed outlier: 3.534A pdb=" N LEU A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2462 removed outlier: 3.663A pdb=" N VAL A2462 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2484 removed outlier: 3.783A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2509 removed outlier: 4.115A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2526 Processing helix chain 'A' and resid 2536 through 2543 removed outlier: 4.123A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2553 through 2564 Processing helix chain 'A' and resid 2790 through 2799 removed outlier: 3.559A pdb=" N GLN A2795 " --> pdb=" O ILE A2791 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 4.114A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.834A pdb=" N LYS A2829 " --> pdb=" O THR A2825 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 3.729A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2874 through 2883 removed outlier: 4.059A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 4.112A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2931 Processing helix chain 'A' and resid 2935 through 2943 removed outlier: 3.924A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) Processing helix chain 'A' and resid 2952 through 2962 removed outlier: 3.793A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2972 through 2977 removed outlier: 3.844A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.737A pdb=" N LYS A2991 " --> pdb=" O THR A2987 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A2993 " --> pdb=" O ALA A2989 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A2995 " --> pdb=" O LYS A2991 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A3005 " --> pdb=" O CYS A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3018 removed outlier: 3.680A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A3018 " --> pdb=" O CYS A3014 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 3.801A pdb=" N GLU A3038 " --> pdb=" O PRO A3034 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.701A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.808A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3077 through 3082 removed outlier: 3.688A pdb=" N TYR A3082 " --> pdb=" O LEU A3078 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3093 Processing helix chain 'A' and resid 3095 through 3116 removed outlier: 3.802A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3197 Processing helix chain 'A' and resid 3227 through 3249 removed outlier: 4.091A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3263 removed outlier: 3.952A pdb=" N ALA A3255 " --> pdb=" O ASN A3251 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3291 removed outlier: 3.832A pdb=" N SER A3290 " --> pdb=" O CYS A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3292 through 3306 removed outlier: 3.847A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) Processing helix chain 'A' and resid 3307 through 3309 No H-bonds generated for 'chain 'A' and resid 3307 through 3309' Processing helix chain 'A' and resid 3319 through 3344 removed outlier: 4.023A pdb=" N SER A3342 " --> pdb=" O ALA A3338 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A3343 " --> pdb=" O ASN A3339 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3361 Processing helix chain 'A' and resid 3373 through 3391 Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.666A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.634A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 4.298A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 Processing helix chain 'A' and resid 3498 through 3503 removed outlier: 4.027A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3525 through 3539 removed outlier: 4.345A pdb=" N ILE A3529 " --> pdb=" O TYR A3525 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR A3531 " --> pdb=" O GLN A3527 " (cutoff:3.500A) Proline residue: A3532 - end of helix removed outlier: 4.011A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A3539 " --> pdb=" O ILE A3535 " (cutoff:3.500A) Processing helix chain 'A' and resid 3546 through 3562 removed outlier: 4.019A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3580 through 3596 removed outlier: 3.824A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.377A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3641 through 3651 removed outlier: 3.862A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3660 through 3670 Processing helix chain 'A' and resid 3759 through 3775 Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 4.224A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.626A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3846 Processing helix chain 'A' and resid 3853 through 3858 Processing helix chain 'A' and resid 3865 through 3876 removed outlier: 3.615A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3892 removed outlier: 3.834A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A3892 " --> pdb=" O VAL A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3918 removed outlier: 4.188A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A3904 " --> pdb=" O LEU A3900 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 3.534A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3992 removed outlier: 3.949A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A3983 " --> pdb=" O LEU A3979 " (cutoff:3.500A) Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4013 through 4023 Processing helix chain 'A' and resid 4041 through 4052 Processing helix chain 'A' and resid 4057 through 4068 removed outlier: 3.828A pdb=" N CYS A4061 " --> pdb=" O ALA A4057 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4088 through 4093 removed outlier: 3.792A pdb=" N GLN A4092 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4121 through 4125 Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA2, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 3.812A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 4.016A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 1451 hydrogen bonds defined for protein. 4299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 19.07 Time building geometry restraints manager: 13.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8455 1.34 - 1.46: 6629 1.46 - 1.58: 14538 1.58 - 1.70: 91 1.70 - 1.83: 287 Bond restraints: 30000 Sorted by residual: bond pdb=" C PRO A2372 " pdb=" N PRO A2373 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.01e+01 bond pdb=" C LEU A 793 " pdb=" N PRO A 794 " ideal model delta sigma weight residual 1.334 1.372 -0.038 8.40e-03 1.42e+04 2.06e+01 bond pdb=" N ARG A 350 " pdb=" CA ARG A 350 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.75e+00 bond pdb=" N THR A 235 " pdb=" CA THR A 235 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.31e-02 5.83e+03 6.92e+00 bond pdb=" N CYS A 232 " pdb=" CA CYS A 232 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.99e+00 ... (remaining 29995 not shown) Histogram of bond angle deviations from ideal: 98.26 - 107.04: 1188 107.04 - 115.83: 18543 115.83 - 124.62: 20303 124.62 - 133.41: 700 133.41 - 142.20: 46 Bond angle restraints: 40780 Sorted by residual: angle pdb=" C PRO A3676 " pdb=" N PRO A3677 " pdb=" CA PRO A3677 " ideal model delta sigma weight residual 119.84 108.48 11.36 1.25e+00 6.40e-01 8.25e+01 angle pdb=" N TRP A4038 " pdb=" CA TRP A4038 " pdb=" C TRP A4038 " ideal model delta sigma weight residual 111.04 99.67 11.37 1.55e+00 4.16e-01 5.38e+01 angle pdb=" C GLU A1002 " pdb=" N SER A1003 " pdb=" CA SER A1003 " ideal model delta sigma weight residual 122.73 132.97 -10.24 1.62e+00 3.81e-01 4.00e+01 angle pdb=" C ALA A 266 " pdb=" N VAL A 267 " pdb=" CA VAL A 267 " ideal model delta sigma weight residual 120.24 124.12 -3.88 6.30e-01 2.52e+00 3.78e+01 angle pdb=" C ASP A4012 " pdb=" N TRP A4013 " pdb=" CA TRP A4013 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 ... (remaining 40775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15495 17.98 - 35.95: 2002 35.95 - 53.93: 481 53.93 - 71.91: 124 71.91 - 89.89: 28 Dihedral angle restraints: 18130 sinusoidal: 7574 harmonic: 10556 Sorted by residual: dihedral pdb=" CA ASP A 607 " pdb=" C ASP A 607 " pdb=" N PRO A 608 " pdb=" CA PRO A 608 " ideal model delta harmonic sigma weight residual 180.00 116.97 63.03 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA PRO A 608 " pdb=" C PRO A 608 " pdb=" N ALA A 609 " pdb=" CA ALA A 609 " ideal model delta harmonic sigma weight residual 180.00 -146.37 -33.63 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA ASN A2534 " pdb=" C ASN A2534 " pdb=" N THR A2535 " pdb=" CA THR A2535 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 18127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3608 0.062 - 0.124: 901 0.124 - 0.186: 151 0.186 - 0.248: 19 0.248 - 0.310: 5 Chirality restraints: 4684 Sorted by residual: chirality pdb=" CA TRP A4038 " pdb=" N TRP A4038 " pdb=" C TRP A4038 " pdb=" CB TRP A4038 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE A3719 " pdb=" CA ILE A3719 " pdb=" CG1 ILE A3719 " pdb=" CG2 ILE A3719 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE A2336 " pdb=" CA ILE A2336 " pdb=" CG1 ILE A2336 " pdb=" CG2 ILE A2336 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 4681 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A2182 " -0.020 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ILE A2182 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE A2182 " -0.029 2.00e-02 2.50e+03 pdb=" N HIS A2183 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1002 " -0.017 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLU A1002 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU A1002 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A1003 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 385 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C TYR A 385 " -0.066 2.00e-02 2.50e+03 pdb=" O TYR A 385 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL A 386 " 0.022 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 7739 2.79 - 3.32: 28165 3.32 - 3.85: 48638 3.85 - 4.37: 53922 4.37 - 4.90: 87356 Nonbonded interactions: 225820 Sorted by model distance: nonbonded pdb=" O ASP A3180 " pdb=" OG1 THR A3184 " model vdw 2.268 2.440 nonbonded pdb=" O ARG A2842 " pdb=" OG1 THR A2846 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A2955 " pdb=" OE1 GLN A2971 " model vdw 2.275 2.440 nonbonded pdb=" O LYS A 133 " pdb=" OG1 THR A 137 " model vdw 2.276 2.440 nonbonded pdb=" O ARG A 532 " pdb=" OG SER A 536 " model vdw 2.278 2.440 ... (remaining 225815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.980 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: 0.030 Extract box with map and model: 10.990 Check model and map are aligned: 0.430 Set scattering table: 0.300 Process input model: 97.200 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 0.077 30000 Z= 0.354 Angle : 1.054 17.196 40780 Z= 0.573 Chirality : 0.056 0.310 4684 Planarity : 0.008 0.090 5000 Dihedral : 17.491 89.886 11246 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.21 % Favored : 87.53 % Rotamer: Outliers : 0.55 % Allowed : 11.57 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.03 % 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: -4.94 (0.11), residues: 3545 helix: -2.72 (0.08), residues: 2244 sheet: -2.91 (0.88), residues: 32 loop : -4.14 (0.14), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A1039 HIS 0.011 0.001 HIS A 738 PHE 0.038 0.002 PHE A1089 TYR 0.021 0.002 TYR A2316 ARG 0.008 0.001 ARG A3741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 441 time to evaluate : 3.626 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 103 TYR cc_start: 0.8753 (m-80) cc_final: 0.8025 (m-10) REVERT: A 238 MET cc_start: 0.8091 (mmt) cc_final: 0.7817 (mmm) REVERT: A 326 MET cc_start: 0.8263 (ptm) cc_final: 0.7913 (ppp) REVERT: A 338 LEU cc_start: 0.9132 (tp) cc_final: 0.8805 (pp) REVERT: A 359 LEU cc_start: 0.8560 (mt) cc_final: 0.8226 (pt) REVERT: A 441 MET cc_start: 0.8427 (tpt) cc_final: 0.7710 (tpp) REVERT: A 959 TYR cc_start: 0.7909 (p90) cc_final: 0.7621 (p90) REVERT: A 961 LEU cc_start: 0.9091 (tp) cc_final: 0.8796 (tt) REVERT: A 963 LYS cc_start: 0.8327 (mttt) cc_final: 0.7301 (tttp) REVERT: A 966 PHE cc_start: 0.8830 (m-10) cc_final: 0.8523 (m-80) REVERT: A 1369 MET cc_start: 0.8791 (mmt) cc_final: 0.8453 (mmp) REVERT: A 1392 MET cc_start: 0.8229 (mtp) cc_final: 0.7994 (mtp) REVERT: A 1804 MET cc_start: 0.9080 (ptm) cc_final: 0.8833 (ptm) REVERT: A 2126 MET cc_start: 0.6213 (ttt) cc_final: 0.5847 (ttm) REVERT: A 2220 MET cc_start: 0.9088 (mtt) cc_final: 0.8881 (mtm) REVERT: A 2255 LEU cc_start: 0.8394 (pt) cc_final: 0.8110 (pt) REVERT: A 2274 ILE cc_start: 0.9241 (pt) cc_final: 0.8988 (pt) REVERT: A 2307 MET cc_start: 0.8146 (tmm) cc_final: 0.7875 (tmm) REVERT: A 2546 TYR cc_start: 0.8265 (t80) cc_final: 0.7931 (t80) REVERT: A 3235 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8313 (mtmm) REVERT: A 3239 LYS cc_start: 0.8605 (mttm) cc_final: 0.8395 (mttm) REVERT: A 3315 TYR cc_start: 0.5277 (t80) cc_final: 0.4802 (t80) REVERT: A 3621 LYS cc_start: 0.9054 (tppt) cc_final: 0.8840 (tppt) REVERT: A 3741 ARG cc_start: 0.7109 (ptp90) cc_final: 0.6337 (ptp90) REVERT: A 3774 ILE cc_start: 0.9156 (mt) cc_final: 0.8948 (mt) outliers start: 17 outliers final: 3 residues processed: 455 average time/residue: 0.4039 time to fit residues: 295.7931 Evaluate side-chains 299 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN A 289 ASN A 322 GLN A 355 ASN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A 454 GLN A 484 HIS A 611 ASN ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN A1598 ASN A1611 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1859 ASN ** A1890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1980 ASN ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN A2352 HIS A2354 ASN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN A2523 ASN A2831 ASN A3093 GLN A3139 GLN ** A3148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 ASN A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3573 ASN A3590 ASN A3671 ASN ** A3908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 HIS ** A4055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30000 Z= 0.286 Angle : 0.751 9.505 40780 Z= 0.397 Chirality : 0.043 0.193 4684 Planarity : 0.006 0.142 5000 Dihedral : 13.690 67.280 4358 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.64 % Favored : 87.31 % Rotamer: Outliers : 0.10 % Allowed : 6.94 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -3.37 (0.13), residues: 3545 helix: -1.36 (0.10), residues: 2275 sheet: -2.51 (0.89), residues: 31 loop : -3.84 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A3164 HIS 0.008 0.001 HIS A 738 PHE 0.045 0.002 PHE A1060 TYR 0.036 0.002 TYR A2288 ARG 0.014 0.000 ARG A2143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 365 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8662 (m-80) cc_final: 0.8053 (m-10) REVERT: A 359 LEU cc_start: 0.8584 (mt) cc_final: 0.8295 (pt) REVERT: A 441 MET cc_start: 0.8296 (tpt) cc_final: 0.7787 (tpp) REVERT: A 963 LYS cc_start: 0.8363 (mttt) cc_final: 0.7503 (tttp) REVERT: A 1369 MET cc_start: 0.8663 (mmt) cc_final: 0.8228 (mmp) REVERT: A 1688 LEU cc_start: 0.8371 (mp) cc_final: 0.8112 (mm) REVERT: A 1804 MET cc_start: 0.9128 (ptm) cc_final: 0.8781 (ptm) REVERT: A 2104 MET cc_start: 0.7101 (mtm) cc_final: 0.6587 (mtp) REVERT: A 2126 MET cc_start: 0.6289 (ttt) cc_final: 0.6035 (ttm) REVERT: A 2274 ILE cc_start: 0.9362 (pt) cc_final: 0.9141 (pt) REVERT: A 2307 MET cc_start: 0.8242 (tmm) cc_final: 0.7950 (tmm) REVERT: A 2546 TYR cc_start: 0.8183 (t80) cc_final: 0.7887 (t80) REVERT: A 2937 ASP cc_start: 0.8900 (m-30) cc_final: 0.8310 (t0) REVERT: A 3235 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8620 (mtpt) REVERT: A 3315 TYR cc_start: 0.5423 (t80) cc_final: 0.5002 (t80) REVERT: A 3808 ASN cc_start: 0.8177 (t0) cc_final: 0.7481 (p0) REVERT: A 3932 MET cc_start: 0.9145 (mtm) cc_final: 0.8863 (mtt) REVERT: A 4020 MET cc_start: 0.8734 (ttm) cc_final: 0.8366 (ttm) outliers start: 3 outliers final: 2 residues processed: 368 average time/residue: 0.4089 time to fit residues: 250.4040 Evaluate side-chains 278 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 272 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 328 optimal weight: 9.9990 chunk 354 optimal weight: 0.1980 chunk 292 optimal weight: 9.9990 chunk 325 optimal weight: 0.0670 chunk 111 optimal weight: 0.3980 chunk 263 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN A 415 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1624 GLN A1830 HIS A1866 GLN A1890 HIS ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2432 GLN ** A2475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2514 ASN A2518 GLN ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3148 GLN A3422 GLN A3423 GLN A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3716 HIS A3748 HIS A3908 HIS A4088 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30000 Z= 0.168 Angle : 0.665 12.607 40780 Z= 0.338 Chirality : 0.040 0.173 4684 Planarity : 0.005 0.072 5000 Dihedral : 13.146 72.384 4358 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.07 % Favored : 89.90 % Rotamer: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -2.43 (0.14), residues: 3545 helix: -0.55 (0.11), residues: 2281 sheet: -2.19 (0.96), residues: 30 loop : -3.65 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A3164 HIS 0.004 0.001 HIS A2426 PHE 0.031 0.001 PHE A1060 TYR 0.025 0.001 TYR A 527 ARG 0.004 0.000 ARG A3046 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 3.528 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 103 TYR cc_start: 0.8581 (m-80) cc_final: 0.8015 (m-80) REVERT: A 326 MET cc_start: 0.8610 (ptt) cc_final: 0.8095 (ppp) REVERT: A 359 LEU cc_start: 0.8474 (mt) cc_final: 0.8250 (pt) REVERT: A 441 MET cc_start: 0.8154 (tpt) cc_final: 0.7746 (tpp) REVERT: A 963 LYS cc_start: 0.8122 (mttt) cc_final: 0.7321 (tttp) REVERT: A 966 PHE cc_start: 0.8751 (m-10) cc_final: 0.8370 (m-10) REVERT: A 1369 MET cc_start: 0.8563 (mmt) cc_final: 0.8145 (mmp) REVERT: A 1804 MET cc_start: 0.9056 (ptm) cc_final: 0.8740 (ptm) REVERT: A 2100 LEU cc_start: 0.9186 (tt) cc_final: 0.8913 (tt) REVERT: A 2102 LYS cc_start: 0.9353 (mttt) cc_final: 0.9022 (mtmm) REVERT: A 2104 MET cc_start: 0.7013 (mtm) cc_final: 0.6694 (mtp) REVERT: A 2126 MET cc_start: 0.6189 (ttt) cc_final: 0.5783 (ttm) REVERT: A 3084 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 3315 TYR cc_start: 0.5225 (t80) cc_final: 0.4799 (t80) REVERT: A 3687 MET cc_start: 0.8404 (pmm) cc_final: 0.7871 (pmm) REVERT: A 3808 ASN cc_start: 0.8201 (t0) cc_final: 0.7588 (p0) REVERT: A 3974 MET cc_start: 0.8471 (mpp) cc_final: 0.7869 (mpp) REVERT: A 4020 MET cc_start: 0.8809 (ttm) cc_final: 0.8457 (ttm) outliers start: 4 outliers final: 1 residues processed: 420 average time/residue: 0.3885 time to fit residues: 272.5439 Evaluate side-chains 298 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 0.1980 chunk 246 optimal weight: 0.6980 chunk 170 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 0.0570 chunk 220 optimal weight: 10.0000 chunk 329 optimal weight: 30.0000 chunk 348 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 94 optimal weight: 0.0040 overall best weight: 0.5912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 ASN A2270 ASN A2475 ASN ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS A3510 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30000 Z= 0.159 Angle : 0.638 14.193 40780 Z= 0.324 Chirality : 0.040 0.228 4684 Planarity : 0.004 0.073 5000 Dihedral : 12.826 72.380 4358 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.52 % Favored : 89.45 % Rotamer: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.14), residues: 3545 helix: -0.13 (0.11), residues: 2277 sheet: -1.94 (0.92), residues: 31 loop : -3.58 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3164 HIS 0.009 0.001 HIS A 738 PHE 0.033 0.001 PHE A 251 TYR 0.038 0.001 TYR A2288 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 421 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5114 (tpp) cc_final: 0.4748 (tpp) REVERT: A 103 TYR cc_start: 0.8475 (m-80) cc_final: 0.7876 (m-10) REVERT: A 189 MET cc_start: 0.6610 (mpp) cc_final: 0.6143 (mpp) REVERT: A 326 MET cc_start: 0.8647 (ptt) cc_final: 0.8027 (ppp) REVERT: A 441 MET cc_start: 0.8167 (tpt) cc_final: 0.7762 (tpp) REVERT: A 718 MET cc_start: 0.7495 (ppp) cc_final: 0.7286 (ppp) REVERT: A 725 LEU cc_start: 0.8046 (pt) cc_final: 0.7836 (pt) REVERT: A 963 LYS cc_start: 0.8113 (mttt) cc_final: 0.7303 (tttp) REVERT: A 966 PHE cc_start: 0.8811 (m-10) cc_final: 0.8436 (m-10) REVERT: A 1199 PRO cc_start: 0.8682 (Cg_exo) cc_final: 0.8438 (Cg_endo) REVERT: A 1369 MET cc_start: 0.8446 (mmt) cc_final: 0.7969 (mmp) REVERT: A 1804 MET cc_start: 0.9109 (ptm) cc_final: 0.8729 (ptm) REVERT: A 2100 LEU cc_start: 0.9190 (tt) cc_final: 0.8954 (tt) REVERT: A 2102 LYS cc_start: 0.9359 (mttt) cc_final: 0.9040 (mtmm) REVERT: A 2104 MET cc_start: 0.6991 (mtm) cc_final: 0.6741 (mtp) REVERT: A 2126 MET cc_start: 0.6133 (ttt) cc_final: 0.5724 (ttm) REVERT: A 2307 MET cc_start: 0.8116 (tmm) cc_final: 0.7829 (tmm) REVERT: A 2443 MET cc_start: 0.5835 (tmm) cc_final: 0.5597 (tmm) REVERT: A 3315 TYR cc_start: 0.5367 (t80) cc_final: 0.4957 (t80) REVERT: A 3414 MET cc_start: 0.8355 (tpt) cc_final: 0.8072 (tpp) REVERT: A 3808 ASN cc_start: 0.7959 (t0) cc_final: 0.7587 (p0) REVERT: A 3974 MET cc_start: 0.8512 (mpp) cc_final: 0.8001 (mpp) REVERT: A 4020 MET cc_start: 0.8808 (ttm) cc_final: 0.8440 (ttm) outliers start: 1 outliers final: 1 residues processed: 422 average time/residue: 0.3813 time to fit residues: 268.3598 Evaluate side-chains 302 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 297 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 313 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A2103 HIS ** A2426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN ** A3423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3660 ASN ** A4055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4087 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30000 Z= 0.321 Angle : 0.755 13.266 40780 Z= 0.393 Chirality : 0.044 0.186 4684 Planarity : 0.005 0.074 5000 Dihedral : 12.999 69.402 4358 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.83 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -2.16 (0.14), residues: 3545 helix: -0.33 (0.11), residues: 2263 sheet: -1.52 (0.88), residues: 36 loop : -3.56 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1039 HIS 0.007 0.001 HIS A 738 PHE 0.027 0.002 PHE A 251 TYR 0.019 0.002 TYR A2316 ARG 0.004 0.001 ARG A1806 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5382 (tpp) cc_final: 0.5014 (tpp) REVERT: A 103 TYR cc_start: 0.8649 (m-80) cc_final: 0.8050 (m-10) REVERT: A 189 MET cc_start: 0.6696 (mpp) cc_final: 0.6115 (mpp) REVERT: A 326 MET cc_start: 0.8689 (ptt) cc_final: 0.8116 (ppp) REVERT: A 357 LYS cc_start: 0.7954 (mttp) cc_final: 0.7752 (mmtt) REVERT: A 441 MET cc_start: 0.8213 (tpt) cc_final: 0.7701 (tpp) REVERT: A 963 LYS cc_start: 0.8448 (mttt) cc_final: 0.7541 (tttp) REVERT: A 1369 MET cc_start: 0.8509 (mmt) cc_final: 0.8019 (mmp) REVERT: A 1724 MET cc_start: 0.8316 (tpp) cc_final: 0.8095 (mmm) REVERT: A 1757 MET cc_start: 0.5990 (tpt) cc_final: 0.5095 (tpt) REVERT: A 1804 MET cc_start: 0.9181 (ptm) cc_final: 0.8790 (ptm) REVERT: A 1927 MET cc_start: 0.7781 (mmp) cc_final: 0.7491 (mmp) REVERT: A 2100 LEU cc_start: 0.9167 (tt) cc_final: 0.8942 (tt) REVERT: A 2102 LYS cc_start: 0.9414 (mttt) cc_final: 0.9153 (mttp) REVERT: A 2104 MET cc_start: 0.7065 (mtm) cc_final: 0.6733 (mtp) REVERT: A 2126 MET cc_start: 0.6297 (ttt) cc_final: 0.5923 (ttm) REVERT: A 2307 MET cc_start: 0.8280 (tmm) cc_final: 0.8050 (tmm) REVERT: A 3242 MET cc_start: 0.7641 (tpp) cc_final: 0.7277 (tpp) REVERT: A 3315 TYR cc_start: 0.5774 (t80) cc_final: 0.5277 (t80) REVERT: A 4020 MET cc_start: 0.8863 (ttm) cc_final: 0.8425 (ttm) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3976 time to fit residues: 237.9022 Evaluate side-chains 264 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 0.0370 chunk 86 optimal weight: 0.0980 chunk 349 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 183 optimal weight: 0.4980 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1866 GLN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2103 HIS ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30000 Z= 0.170 Angle : 0.658 14.991 40780 Z= 0.334 Chirality : 0.041 0.181 4684 Planarity : 0.004 0.068 5000 Dihedral : 12.770 72.846 4358 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.32 % Favored : 89.65 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -1.71 (0.14), residues: 3545 helix: 0.04 (0.11), residues: 2272 sheet: -1.67 (0.93), residues: 31 loop : -3.40 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1039 HIS 0.004 0.001 HIS A 993 PHE 0.032 0.001 PHE A 251 TYR 0.040 0.001 TYR A2288 ARG 0.005 0.000 ARG A1608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 3.421 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 96 MET cc_start: 0.5253 (tpp) cc_final: 0.4955 (tpp) REVERT: A 103 TYR cc_start: 0.8413 (m-80) cc_final: 0.7957 (m-10) REVERT: A 189 MET cc_start: 0.6435 (mpp) cc_final: 0.5935 (mpp) REVERT: A 326 MET cc_start: 0.8585 (ptt) cc_final: 0.8063 (ppp) REVERT: A 441 MET cc_start: 0.8124 (tpt) cc_final: 0.7848 (tpp) REVERT: A 718 MET cc_start: 0.7671 (ppp) cc_final: 0.7455 (ppp) REVERT: A 775 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 963 LYS cc_start: 0.8067 (mttt) cc_final: 0.7298 (tttp) REVERT: A 1369 MET cc_start: 0.8439 (mmt) cc_final: 0.7964 (mmp) REVERT: A 1757 MET cc_start: 0.5979 (tpt) cc_final: 0.5081 (tpt) REVERT: A 1804 MET cc_start: 0.9111 (ptm) cc_final: 0.8757 (ptm) REVERT: A 2098 THR cc_start: 0.8934 (t) cc_final: 0.8582 (t) REVERT: A 2102 LYS cc_start: 0.9385 (mttt) cc_final: 0.9128 (mttp) REVERT: A 2126 MET cc_start: 0.6197 (ttt) cc_final: 0.5867 (ttm) REVERT: A 2307 MET cc_start: 0.8197 (tmm) cc_final: 0.7902 (tmm) REVERT: A 2385 LEU cc_start: 0.8013 (tp) cc_final: 0.7611 (tp) REVERT: A 2443 MET cc_start: 0.5633 (tmm) cc_final: 0.5429 (tmm) REVERT: A 3002 TYR cc_start: 0.7876 (m-80) cc_final: 0.7550 (m-80) REVERT: A 3242 MET cc_start: 0.7474 (tpp) cc_final: 0.7247 (tpp) REVERT: A 3808 ASN cc_start: 0.7939 (t0) cc_final: 0.7565 (p0) REVERT: A 4020 MET cc_start: 0.8848 (ttm) cc_final: 0.8448 (ttm) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.4038 time to fit residues: 268.9431 Evaluate side-chains 301 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 255 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 195 optimal weight: 0.2980 chunk 347 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30000 Z= 0.171 Angle : 0.650 13.903 40780 Z= 0.329 Chirality : 0.040 0.196 4684 Planarity : 0.004 0.068 5000 Dihedral : 12.563 73.852 4358 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.97 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3545 helix: 0.24 (0.11), residues: 2260 sheet: -1.82 (0.88), residues: 31 loop : -3.37 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1039 HIS 0.009 0.001 HIS A 738 PHE 0.031 0.001 PHE A 251 TYR 0.021 0.001 TYR A1558 ARG 0.004 0.000 ARG A2377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.453 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 103 TYR cc_start: 0.8495 (m-80) cc_final: 0.8090 (m-10) REVERT: A 189 MET cc_start: 0.6605 (mpp) cc_final: 0.6005 (mpp) REVERT: A 326 MET cc_start: 0.8558 (ptt) cc_final: 0.8037 (ppp) REVERT: A 441 MET cc_start: 0.8222 (tpt) cc_final: 0.7869 (tpp) REVERT: A 775 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 963 LYS cc_start: 0.8177 (mttt) cc_final: 0.7347 (tttp) REVERT: A 1369 MET cc_start: 0.8337 (mmt) cc_final: 0.7998 (mmp) REVERT: A 1804 MET cc_start: 0.9058 (ptm) cc_final: 0.8651 (ptp) REVERT: A 1933 LEU cc_start: 0.7801 (mt) cc_final: 0.7421 (mt) REVERT: A 2102 LYS cc_start: 0.9383 (mttt) cc_final: 0.9127 (mtmm) REVERT: A 2126 MET cc_start: 0.6419 (ttt) cc_final: 0.6058 (ttm) REVERT: A 2307 MET cc_start: 0.8181 (tmm) cc_final: 0.7899 (tmm) REVERT: A 2331 MET cc_start: 0.7337 (mtm) cc_final: 0.6678 (mtt) REVERT: A 2385 LEU cc_start: 0.8118 (tp) cc_final: 0.7780 (tp) REVERT: A 2843 PHE cc_start: 0.8304 (m-10) cc_final: 0.7821 (m-80) REVERT: A 3002 TYR cc_start: 0.7782 (m-10) cc_final: 0.7542 (m-80) REVERT: A 3242 MET cc_start: 0.7390 (tpp) cc_final: 0.7069 (tpp) REVERT: A 3808 ASN cc_start: 0.8050 (t0) cc_final: 0.7621 (p0) REVERT: A 3959 MET cc_start: 0.8969 (pmm) cc_final: 0.8620 (pmm) REVERT: A 4020 MET cc_start: 0.8814 (ttm) cc_final: 0.8437 (ttm) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3964 time to fit residues: 262.5613 Evaluate side-chains 298 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 104 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 448 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 HIS ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 HIS A2390 HIS ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3249 GLN A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30000 Z= 0.166 Angle : 0.657 13.451 40780 Z= 0.328 Chirality : 0.041 0.305 4684 Planarity : 0.004 0.069 5000 Dihedral : 12.429 73.917 4358 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.21 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 3545 helix: 0.35 (0.11), residues: 2262 sheet: -2.00 (0.85), residues: 31 loop : -3.31 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1039 HIS 0.006 0.001 HIS A 738 PHE 0.034 0.001 PHE A3722 TYR 0.044 0.001 TYR A2288 ARG 0.002 0.000 ARG A3741 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8502 (m-80) cc_final: 0.8105 (m-10) REVERT: A 189 MET cc_start: 0.6527 (mpp) cc_final: 0.5978 (mpp) REVERT: A 326 MET cc_start: 0.8535 (ptt) cc_final: 0.7984 (ppp) REVERT: A 441 MET cc_start: 0.8223 (tpt) cc_final: 0.7949 (tpp) REVERT: A 775 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 963 LYS cc_start: 0.8133 (mttt) cc_final: 0.7219 (tttp) REVERT: A 1011 GLU cc_start: 0.8698 (pp20) cc_final: 0.8319 (pp20) REVERT: A 1194 PHE cc_start: 0.7772 (m-80) cc_final: 0.7560 (m-80) REVERT: A 1369 MET cc_start: 0.8381 (mmt) cc_final: 0.8065 (mmp) REVERT: A 1804 MET cc_start: 0.8993 (ptm) cc_final: 0.8602 (ptp) REVERT: A 1933 LEU cc_start: 0.7860 (mt) cc_final: 0.7441 (mt) REVERT: A 2102 LYS cc_start: 0.9353 (mttt) cc_final: 0.9098 (mtmm) REVERT: A 2126 MET cc_start: 0.6420 (ttt) cc_final: 0.6068 (ttm) REVERT: A 2307 MET cc_start: 0.8204 (tmm) cc_final: 0.7913 (tmm) REVERT: A 2331 MET cc_start: 0.7265 (mtm) cc_final: 0.6618 (mtt) REVERT: A 2385 LEU cc_start: 0.8118 (tp) cc_final: 0.7765 (tp) REVERT: A 2389 PHE cc_start: 0.7326 (m-10) cc_final: 0.7033 (m-10) REVERT: A 2843 PHE cc_start: 0.8272 (m-10) cc_final: 0.7819 (m-80) REVERT: A 3002 TYR cc_start: 0.7863 (m-10) cc_final: 0.7622 (m-80) REVERT: A 3242 MET cc_start: 0.7354 (tpp) cc_final: 0.6952 (tpp) REVERT: A 3315 TYR cc_start: 0.5350 (t80) cc_final: 0.5020 (t80) REVERT: A 3613 MET cc_start: 0.8697 (tpp) cc_final: 0.8391 (tmm) REVERT: A 3959 MET cc_start: 0.8945 (pmm) cc_final: 0.8657 (pmm) REVERT: A 3974 MET cc_start: 0.8381 (mpp) cc_final: 0.7693 (mpp) REVERT: A 4020 MET cc_start: 0.8842 (ttm) cc_final: 0.8459 (ttm) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.3933 time to fit residues: 260.0100 Evaluate side-chains 300 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 0.7980 chunk 333 optimal weight: 0.0980 chunk 304 optimal weight: 0.9990 chunk 324 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 292 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS A1980 ASN ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30000 Z= 0.162 Angle : 0.651 13.300 40780 Z= 0.325 Chirality : 0.040 0.292 4684 Planarity : 0.005 0.087 5000 Dihedral : 12.317 74.134 4358 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.41 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 3545 helix: 0.44 (0.11), residues: 2267 sheet: -1.92 (0.87), residues: 31 loop : -3.25 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP A3164 HIS 0.005 0.001 HIS A 738 PHE 0.031 0.001 PHE A 251 TYR 0.027 0.001 TYR A1558 ARG 0.005 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8435 (m-80) cc_final: 0.8039 (m-10) REVERT: A 189 MET cc_start: 0.6511 (mpp) cc_final: 0.5893 (mpp) REVERT: A 326 MET cc_start: 0.8545 (ptt) cc_final: 0.7993 (ppp) REVERT: A 441 MET cc_start: 0.8200 (tpt) cc_final: 0.7910 (tpp) REVERT: A 775 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 963 LYS cc_start: 0.7968 (mttt) cc_final: 0.7174 (tttp) REVERT: A 1011 GLU cc_start: 0.8642 (pp20) cc_final: 0.8306 (pp20) REVERT: A 1194 PHE cc_start: 0.7765 (m-80) cc_final: 0.7520 (m-80) REVERT: A 1199 PRO cc_start: 0.8561 (Cg_exo) cc_final: 0.8313 (Cg_endo) REVERT: A 1369 MET cc_start: 0.8361 (mmt) cc_final: 0.8000 (mmp) REVERT: A 1558 TYR cc_start: 0.7353 (t80) cc_final: 0.7119 (t80) REVERT: A 1804 MET cc_start: 0.8947 (ptm) cc_final: 0.8588 (ptp) REVERT: A 1933 LEU cc_start: 0.7848 (mt) cc_final: 0.7437 (mt) REVERT: A 2102 LYS cc_start: 0.9350 (mttt) cc_final: 0.9089 (mtmm) REVERT: A 2126 MET cc_start: 0.6386 (ttt) cc_final: 0.6047 (ttm) REVERT: A 2307 MET cc_start: 0.8172 (tmm) cc_final: 0.7892 (tmm) REVERT: A 2331 MET cc_start: 0.7150 (mtm) cc_final: 0.6498 (mtt) REVERT: A 2385 LEU cc_start: 0.8178 (tp) cc_final: 0.7858 (tp) REVERT: A 2389 PHE cc_start: 0.7373 (m-10) cc_final: 0.7073 (m-10) REVERT: A 2843 PHE cc_start: 0.8152 (m-10) cc_final: 0.7730 (m-80) REVERT: A 2892 LEU cc_start: 0.8443 (tp) cc_final: 0.8097 (tp) REVERT: A 3242 MET cc_start: 0.7299 (tpp) cc_final: 0.6983 (tpp) REVERT: A 3315 TYR cc_start: 0.5346 (t80) cc_final: 0.5015 (t80) REVERT: A 3348 LEU cc_start: 0.7636 (pt) cc_final: 0.6450 (tp) REVERT: A 3613 MET cc_start: 0.8658 (tpp) cc_final: 0.8369 (tmm) REVERT: A 3756 GLU cc_start: 0.7526 (mp0) cc_final: 0.7292 (mp0) REVERT: A 3808 ASN cc_start: 0.8094 (t0) cc_final: 0.7593 (p0) REVERT: A 3959 MET cc_start: 0.8924 (pmm) cc_final: 0.8669 (pmm) REVERT: A 3974 MET cc_start: 0.8337 (mpp) cc_final: 0.7686 (mpp) REVERT: A 4020 MET cc_start: 0.8823 (ttm) cc_final: 0.8476 (ttm) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.3786 time to fit residues: 261.4718 Evaluate side-chains 312 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 chunk 209 optimal weight: 0.0470 chunk 162 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 286 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 175 optimal weight: 0.4980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS A1662 ASN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30000 Z= 0.169 Angle : 0.665 13.216 40780 Z= 0.331 Chirality : 0.041 0.292 4684 Planarity : 0.004 0.066 5000 Dihedral : 12.258 73.836 4358 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.24 % Favored : 89.73 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3545 helix: 0.46 (0.11), residues: 2278 sheet: -2.07 (0.85), residues: 31 loop : -3.20 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.001 TRP A3164 HIS 0.006 0.001 HIS A 738 PHE 0.033 0.001 PHE A 251 TYR 0.025 0.001 TYR A1558 ARG 0.005 0.000 ARG A1151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 398 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8450 (m-80) cc_final: 0.8058 (m-10) REVERT: A 189 MET cc_start: 0.6496 (mpp) cc_final: 0.5865 (mpp) REVERT: A 326 MET cc_start: 0.8562 (ptt) cc_final: 0.8055 (ppp) REVERT: A 441 MET cc_start: 0.8215 (tpt) cc_final: 0.7938 (tpp) REVERT: A 775 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7158 (tm-30) REVERT: A 963 LYS cc_start: 0.7953 (mttt) cc_final: 0.7185 (tttp) REVERT: A 1011 GLU cc_start: 0.8630 (pp20) cc_final: 0.8321 (pp20) REVERT: A 1194 PHE cc_start: 0.7770 (m-80) cc_final: 0.7525 (m-80) REVERT: A 1369 MET cc_start: 0.8366 (mmt) cc_final: 0.8017 (mmp) REVERT: A 1804 MET cc_start: 0.9041 (ptm) cc_final: 0.8635 (ptp) REVERT: A 1927 MET cc_start: 0.8041 (mmp) cc_final: 0.7783 (mmp) REVERT: A 1933 LEU cc_start: 0.7783 (mt) cc_final: 0.7401 (mt) REVERT: A 2102 LYS cc_start: 0.9366 (mttt) cc_final: 0.9088 (mtmm) REVERT: A 2126 MET cc_start: 0.6417 (ttt) cc_final: 0.6081 (ttm) REVERT: A 2307 MET cc_start: 0.8205 (tmm) cc_final: 0.7861 (tmm) REVERT: A 2331 MET cc_start: 0.7151 (mtm) cc_final: 0.6500 (mtt) REVERT: A 2385 LEU cc_start: 0.8159 (tp) cc_final: 0.7845 (tp) REVERT: A 2389 PHE cc_start: 0.7353 (m-10) cc_final: 0.7046 (m-10) REVERT: A 2843 PHE cc_start: 0.8172 (m-10) cc_final: 0.7814 (m-80) REVERT: A 3242 MET cc_start: 0.7342 (tpp) cc_final: 0.7016 (tpp) REVERT: A 3315 TYR cc_start: 0.5401 (t80) cc_final: 0.5069 (t80) REVERT: A 3348 LEU cc_start: 0.7627 (pt) cc_final: 0.6440 (tp) REVERT: A 3613 MET cc_start: 0.8657 (tpp) cc_final: 0.8365 (tmm) REVERT: A 3756 GLU cc_start: 0.7533 (mp0) cc_final: 0.7324 (mp0) REVERT: A 3808 ASN cc_start: 0.8083 (t0) cc_final: 0.7602 (p0) REVERT: A 3820 MET cc_start: 0.8580 (ptt) cc_final: 0.8195 (ppp) REVERT: A 3959 MET cc_start: 0.8924 (pmm) cc_final: 0.8715 (pmm) REVERT: A 3974 MET cc_start: 0.8373 (mpp) cc_final: 0.7655 (mpp) REVERT: A 4020 MET cc_start: 0.8824 (ttm) cc_final: 0.8465 (ttm) REVERT: A 4128 MET cc_start: 0.7924 (ptm) cc_final: 0.7357 (ptp) outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.3777 time to fit residues: 254.7476 Evaluate side-chains 308 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 0.0470 chunk 305 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 264 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 294 optimal weight: 0.0570 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.085531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071349 restraints weight = 153850.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072712 restraints weight = 101834.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073646 restraints weight = 74456.760| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30000 Z= 0.160 Angle : 0.658 13.193 40780 Z= 0.325 Chirality : 0.040 0.287 4684 Planarity : 0.004 0.065 5000 Dihedral : 12.168 74.300 4358 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.79 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3545 helix: 0.56 (0.11), residues: 2276 sheet: -2.09 (0.85), residues: 31 loop : -3.23 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.001 TRP A3164 HIS 0.005 0.001 HIS A1687 PHE 0.025 0.001 PHE A 396 TYR 0.024 0.001 TYR A1558 ARG 0.011 0.000 ARG A3629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5992.44 seconds wall clock time: 110 minutes 8.07 seconds (6608.07 seconds total)