Starting phenix.real_space_refine on Sat Apr 13 06:35:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/04_2024/6gh6_0002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/04_2024/6gh6_0002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/04_2024/6gh6_0002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/04_2024/6gh6_0002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/04_2024/6gh6_0002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/04_2024/6gh6_0002.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 96 5.49 5 S 96 5.16 5 C 17252 2.51 5 N 4960 2.21 5 O 5647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 720": "NH1" <-> "NH2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C ARG 1269": "NH1" <-> "NH2" Residue "C ARG 1301": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 709": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 978": "NH1" <-> "NH2" Residue "D ARG 990": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1067": "NH1" <-> "NH2" Residue "D ARG 1075": "NH1" <-> "NH2" Residue "D PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1173": "NH1" <-> "NH2" Residue "D ARG 1174": "NH1" <-> "NH2" Residue "D ARG 1203": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1290": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "D ARG 1373": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28051 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1776 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1729 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 10068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10068 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 333 Chain: "D" Number of atoms: 10063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10063 Classifications: {'peptide': 1334} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 65} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 1279} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 398 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 11, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 206 Chain: "E" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 568 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "M" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1875 Classifications: {'peptide': 315} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 177} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'UNK:plan-1': 51, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 349 Chain: "N" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 988 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "T" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 984 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 14.76, per 1000 atoms: 0.53 Number of scatterers: 28051 At special positions: 0 Unit cell: (137.16, 171.72, 165.24, 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 96 16.00 P 96 15.00 O 5647 8.00 N 4960 7.00 C 17252 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: 10.81 Conformation dependent library (CDL) restraints added in 4.9 seconds 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6558 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 36 sheets defined 38.4% alpha, 11.5% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 9.52 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.970A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.657A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.600A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.829A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.961A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.609A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.064A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.620A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.014A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.060A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.753A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.532A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.700A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 4.083A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.705A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.660A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 removed outlier: 4.112A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.522A pdb=" N GLY C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.548A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 4.435A pdb=" N ASP C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.899A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 613 removed outlier: 4.151A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.160A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.751A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.646A pdb=" N GLN C 686 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.623A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.710A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.575A pdb=" N ALA C 910 " --> pdb=" O GLY C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 979 removed outlier: 4.159A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.538A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.095A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.911A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1177 Processing helix chain 'C' and resid 1191 through 1201 removed outlier: 3.785A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 4.063A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 4.098A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.793A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.511A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.730A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.583A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.530A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.792A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.245A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 376 " --> pdb=" O MET D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.878A pdb=" N GLY D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.022A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.653A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 483 removed outlier: 4.179A pdb=" N LEU D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.713A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 539 removed outlier: 4.328A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.822A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.697A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.741A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 701 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.812A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.365A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 805 removed outlier: 3.875A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.103A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 916 through 925 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.815A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.397A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1291 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.977A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 3.702A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.909A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.561A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.582A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.805A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 164 removed outlier: 3.675A pdb=" N ILE M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.787A pdb=" N ALA M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 207 removed outlier: 4.747A pdb=" N ALA M 207 " --> pdb=" O LEU M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.834A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS M 223 " --> pdb=" O ILE M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 231 removed outlier: 4.592A pdb=" N HIS M 230 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 255 removed outlier: 4.230A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 355 removed outlier: 3.716A pdb=" N SER M 344 " --> pdb=" O LEU M 340 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.960A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 removed outlier: 3.958A pdb=" N GLN M 387 " --> pdb=" O ARG M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 428 Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.642A pdb=" N GLN M 449 " --> pdb=" O MET M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 463 removed outlier: 3.608A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 5.153A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 8.377A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 105 removed outlier: 3.568A pdb=" N LEU B 102 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.440A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.534A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 103 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.534A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 103 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 145 removed outlier: 3.689A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 7.007A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 158 removed outlier: 4.177A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.001A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.796A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.606A pdb=" N VAL C 296 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 336 " --> pdb=" O VAL C 296 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.741A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.741A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.637A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.731A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 724 through 727 removed outlier: 4.896A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.093A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC5, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.974A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.974A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 865 through 866 removed outlier: 3.503A pdb=" N ILE C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1335 through 1336 removed outlier: 3.965A pdb=" N ALA D 23 " --> pdb=" O ASN C1336 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD1, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.488A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 435 through 437 removed outlier: 3.570A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 366 through 369 Processing sheet with id=AD4, first strand: chain 'D' and resid 527 through 528 removed outlier: 7.233A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 959 through 961 removed outlier: 4.311A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1160 through 1163 removed outlier: 4.418A pdb=" N ILE D1162 " --> pdb=" O GLU D1202 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU D1202 " --> pdb=" O ILE D1162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AD9, first strand: chain 'M' and resid 279 through 281 964 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 15.90 Time building geometry restraints manager: 11.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 1 1.13 - 1.30: 4748 1.30 - 1.47: 11003 1.47 - 1.64: 12712 1.64 - 1.81: 170 Bond restraints: 28634 Sorted by residual: bond pdb=" C THR D 514 " pdb=" N ARG D 515 " ideal model delta sigma weight residual 1.329 0.964 0.365 1.36e-02 5.41e+03 7.22e+02 bond pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 1.332 1.507 -0.175 1.40e-02 5.10e+03 1.56e+02 bond pdb=" C THR M 210 " pdb=" N PRO M 211 " ideal model delta sigma weight residual 1.334 1.511 -0.177 2.34e-02 1.83e+03 5.75e+01 bond pdb=" O3' DA T 1 " pdb=" P DG T 2 " ideal model delta sigma weight residual 1.607 1.686 -0.079 1.50e-02 4.44e+03 2.77e+01 bond pdb=" C LYS M 363 " pdb=" N PRO M 364 " ideal model delta sigma weight residual 1.332 1.390 -0.059 1.30e-02 5.92e+03 2.05e+01 ... (remaining 28629 not shown) Histogram of bond angle deviations from ideal: 85.96 - 98.13: 7 98.13 - 110.30: 6660 110.30 - 122.47: 28157 122.47 - 134.64: 4467 134.64 - 146.82: 6 Bond angle restraints: 39297 Sorted by residual: angle pdb=" CA GLU M 356 " pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 116.51 85.96 30.55 1.34e+00 5.57e-01 5.20e+02 angle pdb=" O GLU M 356 " pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 123.12 146.82 -23.70 1.32e+00 5.74e-01 3.22e+02 angle pdb=" C GLU M 356 " pdb=" N GLN M 357 " pdb=" CA GLN M 357 " ideal model delta sigma weight residual 121.54 89.78 31.76 1.91e+00 2.74e-01 2.77e+02 angle pdb=" O3' DC T 5 " pdb=" P DT T 6 " pdb=" O5' DT T 6 " ideal model delta sigma weight residual 104.00 125.91 -21.91 1.50e+00 4.44e-01 2.13e+02 angle pdb=" C5' DC T 5 " pdb=" C4' DC T 5 " pdb=" O4' DC T 5 " ideal model delta sigma weight residual 109.40 128.95 -19.55 1.50e+00 4.44e-01 1.70e+02 ... (remaining 39292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 16615 35.29 - 70.58: 557 70.58 - 105.87: 24 105.87 - 141.17: 3 141.17 - 176.46: 4 Dihedral angle restraints: 17203 sinusoidal: 7047 harmonic: 10156 Sorted by residual: dihedral pdb=" CA ALA C1263 " pdb=" C ALA C1263 " pdb=" N GLN C1264 " pdb=" CA GLN C1264 " ideal model delta harmonic sigma weight residual -180.00 -139.71 -40.29 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA LEU D 343 " pdb=" C LEU D 343 " pdb=" N GLY D 344 " pdb=" CA GLY D 344 " ideal model delta harmonic sigma weight residual 180.00 -146.65 -33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO D1026 " pdb=" C PRO D1026 " pdb=" N VAL D1027 " pdb=" CA VAL D1027 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 17200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 4642 0.206 - 0.411: 25 0.411 - 0.617: 3 0.617 - 0.823: 0 0.823 - 1.028: 1 Chirality restraints: 4671 Sorted by residual: chirality pdb=" C4' DC T 5 " pdb=" C5' DC T 5 " pdb=" O4' DC T 5 " pdb=" C3' DC T 5 " both_signs ideal model delta sigma weight residual False -2.53 -1.50 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C4' DT T 6 " pdb=" C5' DT T 6 " pdb=" O4' DT T 6 " pdb=" C3' DT T 6 " both_signs ideal model delta sigma weight residual False -2.53 -1.94 -0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" CA UNK M 270 " pdb=" N UNK M 270 " pdb=" C UNK M 270 " pdb=" CB UNK M 270 " both_signs ideal model delta sigma weight residual False 2.52 2.02 0.50 2.00e-01 2.50e+01 6.24e+00 ... (remaining 4668 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU M 356 " 0.026 2.00e-02 2.50e+03 7.98e-02 6.37e+01 pdb=" C GLU M 356 " -0.136 2.00e-02 2.50e+03 pdb=" O GLU M 356 " 0.066 2.00e-02 2.50e+03 pdb=" N GLN M 357 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -8 " -0.051 2.00e-02 2.50e+03 2.31e-02 1.60e+01 pdb=" N9 DG N -8 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG N -8 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG N -8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG N -8 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DG N -8 " -0.020 2.00e-02 2.50e+03 pdb=" O6 DG N -8 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG N -8 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DG N -8 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG N -8 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG N -8 " 0.027 2.00e-02 2.50e+03 pdb=" C4 DG N -8 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N -7 " -0.050 2.00e-02 2.50e+03 2.31e-02 1.46e+01 pdb=" N9 DA N -7 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA N -7 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA N -7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA N -7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA N -7 " -0.014 2.00e-02 2.50e+03 pdb=" N6 DA N -7 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA N -7 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DA N -7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA N -7 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DA N -7 " 0.028 2.00e-02 2.50e+03 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 172 2.53 - 3.12: 22138 3.12 - 3.71: 41188 3.71 - 4.31: 55642 4.31 - 4.90: 90379 Nonbonded interactions: 209519 Sorted by model distance: nonbonded pdb=" OE1 GLU D 523 " pdb=" N GLY D 524 " model vdw 1.934 2.520 nonbonded pdb=" C1' DC N -11 " pdb=" OP1 DT N -10 " model vdw 2.124 3.470 nonbonded pdb=" C GLU M 356 " pdb=" C GLN M 357 " model vdw 2.209 2.800 nonbonded pdb=" OG SER C1322 " pdb=" NZ LYS D 332 " model vdw 2.215 2.520 nonbonded pdb=" C4' DA N -12 " pdb=" OP1 DC N -11 " model vdw 2.220 3.470 ... (remaining 209514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 65 or (resid 66 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resi \ d 71 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 134 or (resid 135 through 138 and (name N or name CA o \ r name C or name O or name CB )) or resid 139 through 142 or (resid 143 and (nam \ e N or name CA or name C or name O or name CB )) or resid 144 through 159 or (re \ sid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 or \ (resid 162 through 166 and (name N or name CA or name C or name O or name CB )) \ or resid 167 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB )) or resid 171 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 232 or (resid 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 through 237)) selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 71 or (resid 72 and (name N or name CA or name C or name O \ or name CB )) or resid 73 through 92 or (resid 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 or (resid 95 and (name N or name CA or na \ me C or name O or name CB )) or resid 96 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 or (resid 193 and (name \ N or name CA or name C or name O or name CB )) or resid 194 through 236 or (res \ id 237 and (name N or name CA or name C or name O or name CB )))) } 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=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.110 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 83.160 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.365 28634 Z= 0.276 Angle : 0.910 31.765 39297 Z= 0.551 Chirality : 0.051 1.028 4671 Planarity : 0.004 0.080 4826 Dihedral : 14.496 176.458 10645 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.75 % Favored : 89.33 % Rotamer: Outliers : 0.38 % Allowed : 1.49 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -3.61 (0.11), residues: 3458 helix: -2.82 (0.11), residues: 1112 sheet: -1.21 (0.26), residues: 285 loop : -2.40 (0.11), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1193 HIS 0.006 0.001 HIS D 104 PHE 0.015 0.001 PHE C 828 TYR 0.013 0.001 TYR C1229 ARG 0.006 0.000 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 570 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8252 (mt) cc_final: 0.7511 (mt) REVERT: A 51 MET cc_start: 0.8819 (mmm) cc_final: 0.8549 (mmm) REVERT: A 80 GLU cc_start: 0.9072 (tt0) cc_final: 0.8842 (tt0) REVERT: A 97 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8477 (tm-30) REVERT: A 115 ILE cc_start: 0.9595 (mt) cc_final: 0.9225 (tp) REVERT: A 173 VAL cc_start: 0.9058 (m) cc_final: 0.8429 (p) REVERT: B 29 GLU cc_start: 0.9433 (tt0) cc_final: 0.9155 (tt0) REVERT: B 77 ASP cc_start: 0.9687 (t0) cc_final: 0.9447 (t70) REVERT: B 147 GLN cc_start: 0.9538 (pt0) cc_final: 0.9204 (pp30) REVERT: B 199 ASP cc_start: 0.8543 (m-30) cc_final: 0.8025 (m-30) REVERT: B 212 ASP cc_start: 0.8891 (t0) cc_final: 0.8458 (t0) REVERT: C 124 MET cc_start: 0.9053 (ptp) cc_final: 0.8776 (ptp) REVERT: C 562 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9079 (mt-10) REVERT: C 741 MET cc_start: 0.9205 (ttm) cc_final: 0.8654 (ttm) REVERT: C 816 ILE cc_start: 0.8893 (mt) cc_final: 0.8534 (tt) REVERT: C 876 GLU cc_start: 0.9423 (tt0) cc_final: 0.9172 (mp0) REVERT: C 1046 VAL cc_start: 0.8958 (p) cc_final: 0.8737 (m) REVERT: C 1199 LEU cc_start: 0.9070 (tt) cc_final: 0.8596 (tp) REVERT: C 1226 THR cc_start: 0.9053 (p) cc_final: 0.8738 (t) REVERT: C 1297 ASP cc_start: 0.7788 (t0) cc_final: 0.6968 (t70) REVERT: C 1319 MET cc_start: 0.7962 (ptp) cc_final: 0.7717 (mtm) REVERT: C 1323 PHE cc_start: 0.8682 (t80) cc_final: 0.8438 (t80) REVERT: D 337 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7527 (mpp-170) REVERT: D 461 PHE cc_start: 0.8295 (m-10) cc_final: 0.7682 (m-80) REVERT: D 641 ILE cc_start: 0.9257 (pt) cc_final: 0.8833 (tp) REVERT: D 686 TRP cc_start: 0.7582 (m100) cc_final: 0.7365 (m100) REVERT: D 701 LEU cc_start: 0.5972 (mt) cc_final: 0.5653 (tt) REVERT: D 786 THR cc_start: 0.8602 (m) cc_final: 0.7782 (p) REVERT: D 901 ARG cc_start: 0.7375 (tpt90) cc_final: 0.6905 (tpm170) REVERT: D 917 VAL cc_start: 0.9105 (m) cc_final: 0.8029 (t) REVERT: D 918 ILE cc_start: 0.8322 (pt) cc_final: 0.7874 (mt) REVERT: D 1040 MET cc_start: 0.5240 (mtm) cc_final: 0.4822 (mtt) REVERT: E 5 THR cc_start: 0.9146 (m) cc_final: 0.8822 (t) REVERT: E 53 GLU cc_start: 0.9611 (mt-10) cc_final: 0.9324 (mt-10) REVERT: E 59 ILE cc_start: 0.8815 (mm) cc_final: 0.8583 (mt) REVERT: M 133 PHE cc_start: 0.1967 (m-10) cc_final: 0.1623 (m-10) REVERT: M 205 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8162 (mp10) outliers start: 10 outliers final: 3 residues processed: 580 average time/residue: 0.4199 time to fit residues: 379.0323 Evaluate side-chains 294 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 40.0000 chunk 150 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 183 optimal weight: 50.0000 chunk 145 optimal weight: 10.0000 chunk 281 optimal weight: 50.0000 chunk 108 optimal weight: 0.5980 chunk 171 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 326 optimal weight: 30.0000 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 132 HIS B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 582 ASN C 604 HIS C 686 GLN C 760 ASN C 799 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN C1264 GLN D 94 GLN D 104 HIS D 209 ASN D 702 GLN D 897 HIS ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 28634 Z= 0.369 Angle : 0.756 10.809 39297 Z= 0.398 Chirality : 0.046 0.232 4671 Planarity : 0.005 0.078 4826 Dihedral : 17.810 179.118 4819 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.06 % Rotamer: Outliers : 0.23 % Allowed : 3.01 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -2.24 (0.13), residues: 3458 helix: -0.65 (0.14), residues: 1167 sheet: -0.74 (0.28), residues: 286 loop : -2.20 (0.12), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1276 HIS 0.006 0.001 HIS D 104 PHE 0.025 0.002 PHE D 437 TYR 0.043 0.002 TYR C 810 ARG 0.009 0.001 ARG C1034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 305 time to evaluate : 3.098 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9517 (tt) cc_final: 0.9313 (tp) REVERT: A 76 GLU cc_start: 0.9370 (mp0) cc_final: 0.9143 (mp0) REVERT: A 97 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8703 (tm-30) REVERT: B 29 GLU cc_start: 0.9634 (tt0) cc_final: 0.9347 (tm-30) REVERT: B 196 THR cc_start: 0.8857 (p) cc_final: 0.8497 (t) REVERT: B 212 ASP cc_start: 0.9161 (t0) cc_final: 0.8804 (t0) REVERT: B 236 ASP cc_start: 0.8559 (t70) cc_final: 0.8094 (p0) REVERT: C 459 MET cc_start: 0.9377 (mtt) cc_final: 0.9133 (mtt) REVERT: C 876 GLU cc_start: 0.9628 (tt0) cc_final: 0.9256 (mp0) REVERT: C 1199 LEU cc_start: 0.9125 (tt) cc_final: 0.8761 (tp) REVERT: D 180 MET cc_start: 0.8333 (tpp) cc_final: 0.8058 (tpt) REVERT: D 470 VAL cc_start: 0.9754 (t) cc_final: 0.9382 (p) REVERT: D 500 ILE cc_start: 0.8828 (tt) cc_final: 0.8534 (pt) REVERT: D 701 LEU cc_start: 0.6086 (mt) cc_final: 0.5583 (tp) REVERT: D 743 MET cc_start: 0.8452 (mtp) cc_final: 0.7662 (mmm) REVERT: D 786 THR cc_start: 0.8418 (m) cc_final: 0.7642 (p) REVERT: D 801 VAL cc_start: 0.9756 (t) cc_final: 0.9453 (p) REVERT: D 839 VAL cc_start: 0.9409 (t) cc_final: 0.8991 (p) REVERT: D 901 ARG cc_start: 0.7860 (tpt90) cc_final: 0.7253 (tpm170) REVERT: D 1040 MET cc_start: 0.5209 (mtm) cc_final: 0.4886 (mtt) REVERT: E 5 THR cc_start: 0.9125 (m) cc_final: 0.8850 (t) REVERT: E 53 GLU cc_start: 0.9558 (mt-10) cc_final: 0.9076 (mt-10) REVERT: E 59 ILE cc_start: 0.8581 (mm) cc_final: 0.7991 (tp) REVERT: M 126 TRP cc_start: 0.8945 (t60) cc_final: 0.8718 (t60) REVERT: M 205 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8137 (mp10) outliers start: 6 outliers final: 2 residues processed: 311 average time/residue: 0.4107 time to fit residues: 205.8701 Evaluate side-chains 227 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 181 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 89 optimal weight: 0.0670 chunk 326 optimal weight: 8.9990 chunk 352 optimal weight: 20.0000 chunk 290 optimal weight: 0.7980 chunk 323 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 262 optimal weight: 9.9990 overall best weight: 1.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 419 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28634 Z= 0.185 Angle : 0.619 10.665 39297 Z= 0.323 Chirality : 0.042 0.242 4671 Planarity : 0.004 0.062 4826 Dihedral : 17.460 179.935 4819 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.24 % Favored : 91.15 % Rotamer: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -1.61 (0.13), residues: 3458 helix: 0.21 (0.15), residues: 1183 sheet: -0.42 (0.30), residues: 266 loop : -2.06 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 807 HIS 0.017 0.001 HIS C1023 PHE 0.011 0.001 PHE D 172 TYR 0.021 0.001 TYR C1229 ARG 0.003 0.000 ARG D1355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 286 time to evaluate : 2.924 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9302 (mp0) cc_final: 0.9016 (mt-10) REVERT: A 97 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8661 (tm-30) REVERT: B 196 THR cc_start: 0.8857 (p) cc_final: 0.8563 (t) REVERT: B 212 ASP cc_start: 0.9241 (t0) cc_final: 0.8903 (t0) REVERT: B 236 ASP cc_start: 0.8461 (t70) cc_final: 0.7972 (p0) REVERT: C 459 MET cc_start: 0.9353 (mtt) cc_final: 0.9102 (mtt) REVERT: C 876 GLU cc_start: 0.9552 (tt0) cc_final: 0.9188 (mp0) REVERT: C 1199 LEU cc_start: 0.9087 (tt) cc_final: 0.8641 (tp) REVERT: D 180 MET cc_start: 0.8306 (tpp) cc_final: 0.8071 (tpt) REVERT: D 339 ARG cc_start: 0.8438 (ttp80) cc_final: 0.7481 (mpt-90) REVERT: D 470 VAL cc_start: 0.9718 (t) cc_final: 0.9375 (p) REVERT: D 500 ILE cc_start: 0.8758 (tt) cc_final: 0.8415 (pt) REVERT: D 743 MET cc_start: 0.8445 (mtp) cc_final: 0.7642 (mmm) REVERT: D 786 THR cc_start: 0.8033 (m) cc_final: 0.7503 (p) REVERT: D 801 VAL cc_start: 0.9713 (t) cc_final: 0.9381 (p) REVERT: D 839 VAL cc_start: 0.9443 (t) cc_final: 0.9104 (p) REVERT: D 901 ARG cc_start: 0.7663 (tpt90) cc_final: 0.7067 (tpm170) REVERT: D 1040 MET cc_start: 0.5168 (mtm) cc_final: 0.4506 (mmm) REVERT: D 1266 ILE cc_start: 0.8994 (pt) cc_final: 0.8418 (tp) REVERT: D 1351 VAL cc_start: 0.9072 (t) cc_final: 0.8421 (p) REVERT: E 5 THR cc_start: 0.9114 (m) cc_final: 0.8819 (t) REVERT: E 41 GLU cc_start: 0.8849 (tt0) cc_final: 0.8616 (pp20) REVERT: E 53 GLU cc_start: 0.9518 (mt-10) cc_final: 0.9014 (mt-10) REVERT: E 59 ILE cc_start: 0.8442 (mm) cc_final: 0.7715 (tp) REVERT: M 205 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8183 (mp10) outliers start: 3 outliers final: 2 residues processed: 289 average time/residue: 0.3789 time to fit residues: 180.0350 Evaluate side-chains 219 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 217 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 322 optimal weight: 7.9990 chunk 245 optimal weight: 40.0000 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 219 optimal weight: 0.0570 chunk 327 optimal weight: 1.9990 chunk 347 optimal weight: 0.0070 chunk 171 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28634 Z= 0.160 Angle : 0.594 10.350 39297 Z= 0.308 Chirality : 0.042 0.210 4671 Planarity : 0.004 0.055 4826 Dihedral : 17.210 177.312 4819 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.16 % Favored : 91.21 % Rotamer: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -1.27 (0.14), residues: 3458 helix: 0.68 (0.15), residues: 1199 sheet: -0.57 (0.29), residues: 296 loop : -1.96 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1020 HIS 0.003 0.001 HIS B 23 PHE 0.011 0.001 PHE D 172 TYR 0.034 0.001 TYR D 360 ARG 0.003 0.000 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.734 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8665 (tm-30) REVERT: B 196 THR cc_start: 0.8928 (p) cc_final: 0.8616 (t) REVERT: B 212 ASP cc_start: 0.9229 (t0) cc_final: 0.8920 (t0) REVERT: B 236 ASP cc_start: 0.8466 (t70) cc_final: 0.7934 (p0) REVERT: C 459 MET cc_start: 0.9346 (mtt) cc_final: 0.9076 (mtt) REVERT: C 876 GLU cc_start: 0.9538 (tt0) cc_final: 0.9180 (mp0) REVERT: C 1199 LEU cc_start: 0.9094 (tt) cc_final: 0.8655 (tp) REVERT: D 180 MET cc_start: 0.8228 (tpp) cc_final: 0.8002 (tpt) REVERT: D 192 MET cc_start: 0.9573 (mtm) cc_final: 0.9335 (ptp) REVERT: D 339 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7538 (ttm110) REVERT: D 470 VAL cc_start: 0.9709 (t) cc_final: 0.9375 (p) REVERT: D 500 ILE cc_start: 0.8694 (tt) cc_final: 0.8352 (pt) REVERT: D 743 MET cc_start: 0.8529 (mtp) cc_final: 0.7695 (mmm) REVERT: D 801 VAL cc_start: 0.9730 (t) cc_final: 0.9411 (p) REVERT: D 901 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7067 (tpm170) REVERT: D 1040 MET cc_start: 0.5178 (mtm) cc_final: 0.4867 (mtt) REVERT: E 5 THR cc_start: 0.9193 (m) cc_final: 0.8875 (t) REVERT: E 41 GLU cc_start: 0.8871 (tt0) cc_final: 0.8620 (pp20) REVERT: E 53 GLU cc_start: 0.9522 (mt-10) cc_final: 0.9004 (mt-10) REVERT: E 59 ILE cc_start: 0.8361 (mm) cc_final: 0.7531 (tp) REVERT: M 205 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8259 (mp10) outliers start: 1 outliers final: 1 residues processed: 284 average time/residue: 0.3983 time to fit residues: 186.0454 Evaluate side-chains 216 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 289 optimal weight: 9.9990 chunk 196 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 296 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 311 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 overall best weight: 4.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN D 266 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28634 Z= 0.329 Angle : 0.687 10.087 39297 Z= 0.358 Chirality : 0.044 0.213 4671 Planarity : 0.004 0.058 4826 Dihedral : 17.375 175.331 4819 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.88 % Favored : 90.46 % Rotamer: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -1.21 (0.14), residues: 3458 helix: 0.82 (0.15), residues: 1196 sheet: -0.72 (0.27), residues: 332 loop : -1.98 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D1020 HIS 0.012 0.001 HIS C1023 PHE 0.019 0.002 PHE C1270 TYR 0.025 0.002 TYR C1229 ARG 0.009 0.001 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 3.190 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 ASP cc_start: 0.9330 (t0) cc_final: 0.9051 (t0) REVERT: B 236 ASP cc_start: 0.8568 (t70) cc_final: 0.8102 (p0) REVERT: C 370 MET cc_start: 0.8719 (mmp) cc_final: 0.8431 (mmm) REVERT: C 459 MET cc_start: 0.9371 (mtt) cc_final: 0.9097 (mtt) REVERT: C 510 GLN cc_start: 0.9085 (pt0) cc_final: 0.8815 (mp10) REVERT: C 876 GLU cc_start: 0.9622 (tt0) cc_final: 0.9155 (mp0) REVERT: C 1199 LEU cc_start: 0.9101 (tt) cc_final: 0.8737 (tp) REVERT: D 102 MET cc_start: 0.8846 (pmm) cc_final: 0.8613 (pmm) REVERT: D 192 MET cc_start: 0.9540 (mtm) cc_final: 0.9250 (mtt) REVERT: D 744 ARG cc_start: 0.8442 (tpt170) cc_final: 0.8222 (tpp80) REVERT: D 801 VAL cc_start: 0.9759 (t) cc_final: 0.9478 (p) REVERT: D 839 VAL cc_start: 0.9373 (t) cc_final: 0.9028 (p) REVERT: D 1040 MET cc_start: 0.5230 (mtm) cc_final: 0.4852 (mtt) REVERT: D 1351 VAL cc_start: 0.9218 (t) cc_final: 0.8744 (p) REVERT: E 5 THR cc_start: 0.9171 (m) cc_final: 0.8936 (t) REVERT: E 15 ASN cc_start: 0.8537 (t0) cc_final: 0.8150 (t0) REVERT: E 41 GLU cc_start: 0.8782 (tt0) cc_final: 0.8513 (pp20) REVERT: E 53 GLU cc_start: 0.9579 (mt-10) cc_final: 0.9071 (mt-10) REVERT: E 59 ILE cc_start: 0.8377 (mm) cc_final: 0.7395 (tp) REVERT: M 205 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8348 (mp10) outliers start: 2 outliers final: 2 residues processed: 256 average time/residue: 0.4064 time to fit residues: 169.2067 Evaluate side-chains 193 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 116 optimal weight: 6.9990 chunk 312 optimal weight: 0.9980 chunk 68 optimal weight: 30.0000 chunk 203 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 347 optimal weight: 0.0040 chunk 288 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28634 Z= 0.151 Angle : 0.612 9.911 39297 Z= 0.314 Chirality : 0.042 0.212 4671 Planarity : 0.004 0.089 4826 Dihedral : 17.213 175.829 4819 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.07 % Favored : 91.27 % Rotamer: Outliers : 0.08 % Allowed : 1.37 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -0.92 (0.14), residues: 3458 helix: 1.19 (0.15), residues: 1198 sheet: -0.44 (0.28), residues: 324 loop : -1.92 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1020 HIS 0.015 0.001 HIS C1023 PHE 0.018 0.001 PHE C 828 TYR 0.026 0.001 TYR D 360 ARG 0.003 0.000 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 2.813 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 ASP cc_start: 0.9567 (t0) cc_final: 0.9281 (t0) REVERT: B 212 ASP cc_start: 0.9307 (t0) cc_final: 0.9032 (t0) REVERT: B 236 ASP cc_start: 0.8430 (t70) cc_final: 0.7962 (p0) REVERT: C 459 MET cc_start: 0.9377 (mtt) cc_final: 0.9106 (mtt) REVERT: C 798 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: C 876 GLU cc_start: 0.9536 (tt0) cc_final: 0.9176 (mp0) REVERT: C 1199 LEU cc_start: 0.9060 (tt) cc_final: 0.8607 (tp) REVERT: D 102 MET cc_start: 0.8851 (pmm) cc_final: 0.8647 (pmm) REVERT: D 470 VAL cc_start: 0.9769 (t) cc_final: 0.9503 (p) REVERT: D 485 MET cc_start: 0.9236 (tpp) cc_final: 0.9007 (tpp) REVERT: D 500 ILE cc_start: 0.8707 (tt) cc_final: 0.8503 (pt) REVERT: D 641 ILE cc_start: 0.9051 (pt) cc_final: 0.8648 (tp) REVERT: D 743 MET cc_start: 0.7999 (ttm) cc_final: 0.7679 (mmm) REVERT: D 801 VAL cc_start: 0.9751 (t) cc_final: 0.9440 (p) REVERT: D 839 VAL cc_start: 0.9434 (t) cc_final: 0.9096 (p) REVERT: D 1040 MET cc_start: 0.5207 (mtm) cc_final: 0.4554 (mmm) REVERT: D 1351 VAL cc_start: 0.9144 (t) cc_final: 0.8556 (p) REVERT: E 5 THR cc_start: 0.9259 (m) cc_final: 0.8818 (t) REVERT: E 15 ASN cc_start: 0.8512 (t0) cc_final: 0.8185 (t0) REVERT: E 41 GLU cc_start: 0.8782 (tt0) cc_final: 0.8518 (pp20) REVERT: E 53 GLU cc_start: 0.9546 (mt-10) cc_final: 0.9077 (mt-10) REVERT: E 59 ILE cc_start: 0.8436 (mm) cc_final: 0.7503 (tp) REVERT: M 205 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8241 (mp10) outliers start: 2 outliers final: 1 residues processed: 266 average time/residue: 0.3968 time to fit residues: 171.0268 Evaluate side-chains 210 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 334 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 253 optimal weight: 30.0000 chunk 196 optimal weight: 20.0000 chunk 292 optimal weight: 0.1980 chunk 193 optimal weight: 4.9990 chunk 346 optimal weight: 40.0000 chunk 216 optimal weight: 6.9990 chunk 210 optimal weight: 0.0070 chunk 159 optimal weight: 9.9990 overall best weight: 3.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28634 Z= 0.318 Angle : 0.683 10.177 39297 Z= 0.354 Chirality : 0.044 0.214 4671 Planarity : 0.004 0.061 4826 Dihedral : 17.335 177.517 4819 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.37 % Favored : 90.02 % Rotamer: Outliers : 0.04 % Allowed : 1.10 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -0.98 (0.14), residues: 3458 helix: 1.13 (0.15), residues: 1202 sheet: -0.45 (0.28), residues: 326 loop : -1.97 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1020 HIS 0.013 0.001 HIS C1023 PHE 0.016 0.002 PHE C1270 TYR 0.027 0.002 TYR C1149 ARG 0.007 0.001 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 ASP cc_start: 0.9374 (t0) cc_final: 0.9109 (t0) REVERT: B 236 ASP cc_start: 0.8575 (t70) cc_final: 0.8125 (p0) REVERT: C 459 MET cc_start: 0.9400 (mtt) cc_final: 0.9127 (mtt) REVERT: C 876 GLU cc_start: 0.9614 (tt0) cc_final: 0.9225 (mp0) REVERT: C 1199 LEU cc_start: 0.9096 (tt) cc_final: 0.8749 (tp) REVERT: C 1281 TYR cc_start: 0.9004 (m-10) cc_final: 0.8643 (m-10) REVERT: D 102 MET cc_start: 0.8846 (pmm) cc_final: 0.8619 (pmm) REVERT: D 151 MET cc_start: 0.8819 (pmm) cc_final: 0.8613 (pmm) REVERT: D 641 ILE cc_start: 0.9021 (pt) cc_final: 0.8584 (tp) REVERT: D 801 VAL cc_start: 0.9785 (t) cc_final: 0.9524 (p) REVERT: D 839 VAL cc_start: 0.9398 (t) cc_final: 0.9038 (p) REVERT: D 1040 MET cc_start: 0.5283 (mtm) cc_final: 0.4904 (mtt) REVERT: D 1351 VAL cc_start: 0.9206 (t) cc_final: 0.8722 (p) REVERT: E 15 ASN cc_start: 0.8647 (t0) cc_final: 0.8199 (t0) REVERT: E 41 GLU cc_start: 0.8731 (tt0) cc_final: 0.8528 (pp20) REVERT: E 53 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9160 (mt-10) REVERT: E 59 ILE cc_start: 0.8468 (mm) cc_final: 0.7693 (tp) REVERT: M 205 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8314 (mp10) outliers start: 1 outliers final: 1 residues processed: 237 average time/residue: 0.3922 time to fit residues: 151.9851 Evaluate side-chains 181 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 171 optimal weight: 0.0170 chunk 32 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS C1268 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28634 Z= 0.214 Angle : 0.618 10.476 39297 Z= 0.321 Chirality : 0.042 0.184 4671 Planarity : 0.004 0.058 4826 Dihedral : 17.291 178.232 4819 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.59 % Favored : 90.78 % Rotamer: Outliers : 0.04 % Allowed : 0.76 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -0.88 (0.14), residues: 3458 helix: 1.25 (0.15), residues: 1206 sheet: -0.57 (0.29), residues: 316 loop : -1.90 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1020 HIS 0.013 0.001 HIS C1023 PHE 0.012 0.001 PHE D 172 TYR 0.026 0.001 TYR C1229 ARG 0.007 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 3.279 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.9325 (ttm) cc_final: 0.9108 (ttp) REVERT: B 212 ASP cc_start: 0.9346 (t0) cc_final: 0.9077 (t0) REVERT: B 236 ASP cc_start: 0.8553 (t70) cc_final: 0.8082 (p0) REVERT: C 459 MET cc_start: 0.9393 (mtt) cc_final: 0.9116 (mtt) REVERT: C 876 GLU cc_start: 0.9542 (tt0) cc_final: 0.9158 (mp0) REVERT: C 1199 LEU cc_start: 0.9088 (tt) cc_final: 0.8658 (tp) REVERT: C 1232 MET cc_start: 0.9163 (mtp) cc_final: 0.8834 (mtp) REVERT: D 102 MET cc_start: 0.8864 (pmm) cc_final: 0.8627 (pmm) REVERT: D 151 MET cc_start: 0.8826 (pmm) cc_final: 0.8616 (pmm) REVERT: D 743 MET cc_start: 0.8492 (tpp) cc_final: 0.7730 (mmm) REVERT: D 801 VAL cc_start: 0.9773 (t) cc_final: 0.9500 (p) REVERT: D 839 VAL cc_start: 0.9399 (t) cc_final: 0.9029 (p) REVERT: D 1040 MET cc_start: 0.5407 (mtm) cc_final: 0.5028 (mtt) REVERT: D 1260 MET cc_start: 0.8898 (tpp) cc_final: 0.8596 (mmm) REVERT: D 1351 VAL cc_start: 0.9164 (t) cc_final: 0.8623 (p) REVERT: E 53 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9190 (mt-10) REVERT: E 59 ILE cc_start: 0.8464 (mm) cc_final: 0.7734 (tp) REVERT: M 205 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8275 (mp10) outliers start: 1 outliers final: 1 residues processed: 237 average time/residue: 0.3872 time to fit residues: 152.5836 Evaluate side-chains 184 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 331 optimal weight: 40.0000 chunk 302 optimal weight: 7.9990 chunk 322 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 253 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 291 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D1227 HIS M 118 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 28634 Z= 0.508 Angle : 0.806 9.650 39297 Z= 0.419 Chirality : 0.048 0.308 4671 Planarity : 0.005 0.063 4826 Dihedral : 17.698 179.532 4819 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.56 % Favored : 88.87 % Rotamer: Outliers : 0.04 % Allowed : 0.91 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3458 helix: 0.88 (0.15), residues: 1211 sheet: -1.08 (0.27), residues: 337 loop : -2.09 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D1020 HIS 0.011 0.002 HIS C1023 PHE 0.020 0.002 PHE C1270 TYR 0.036 0.002 TYR C1229 ARG 0.008 0.001 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 2.955 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.9407 (mtt) cc_final: 0.9142 (mtt) REVERT: C 876 GLU cc_start: 0.9614 (tt0) cc_final: 0.9203 (mp0) REVERT: C 1199 LEU cc_start: 0.9138 (tt) cc_final: 0.8740 (tp) REVERT: D 102 MET cc_start: 0.8978 (pmm) cc_final: 0.8759 (pmm) REVERT: D 743 MET cc_start: 0.8365 (tpp) cc_final: 0.7817 (mmm) REVERT: D 801 VAL cc_start: 0.9792 (t) cc_final: 0.9571 (p) REVERT: D 839 VAL cc_start: 0.9343 (t) cc_final: 0.8960 (p) REVERT: D 1040 MET cc_start: 0.5063 (mtm) cc_final: 0.4710 (mtt) REVERT: D 1260 MET cc_start: 0.9005 (tpp) cc_final: 0.8750 (mmm) REVERT: E 15 ASN cc_start: 0.8573 (t0) cc_final: 0.8216 (t0) REVERT: E 53 GLU cc_start: 0.9622 (mt-10) cc_final: 0.9167 (mt-10) REVERT: E 59 ILE cc_start: 0.8272 (mm) cc_final: 0.7554 (tp) REVERT: M 126 TRP cc_start: 0.8921 (t60) cc_final: 0.8691 (t60) REVERT: M 205 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8296 (mp10) outliers start: 1 outliers final: 1 residues processed: 204 average time/residue: 0.3761 time to fit residues: 127.5658 Evaluate side-chains 167 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 340 optimal weight: 50.0000 chunk 208 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 357 optimal weight: 20.0000 chunk 329 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 226 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 435 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28634 Z= 0.268 Angle : 0.668 12.167 39297 Z= 0.348 Chirality : 0.044 0.270 4671 Planarity : 0.004 0.057 4826 Dihedral : 17.591 179.854 4819 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.20 % Favored : 90.23 % Rotamer: Outliers : 0.04 % Allowed : 0.38 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -1.13 (0.14), residues: 3458 helix: 1.09 (0.15), residues: 1205 sheet: -1.01 (0.28), residues: 318 loop : -2.02 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D1020 HIS 0.012 0.001 HIS C1023 PHE 0.013 0.001 PHE C1270 TYR 0.031 0.002 TYR C1229 ARG 0.009 0.001 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 3.122 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.9423 (mtt) cc_final: 0.9163 (mtt) REVERT: C 828 PHE cc_start: 0.6576 (p90) cc_final: 0.6350 (p90) REVERT: C 876 GLU cc_start: 0.9569 (tt0) cc_final: 0.9172 (mp0) REVERT: C 1199 LEU cc_start: 0.9114 (tt) cc_final: 0.8670 (tp) REVERT: D 102 MET cc_start: 0.8978 (pmm) cc_final: 0.8746 (pmm) REVERT: D 743 MET cc_start: 0.8419 (tpp) cc_final: 0.7877 (mmm) REVERT: D 801 VAL cc_start: 0.9794 (t) cc_final: 0.9549 (p) REVERT: D 1040 MET cc_start: 0.5053 (mtm) cc_final: 0.4675 (mtt) REVERT: E 42 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7451 (mp0) REVERT: E 53 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9130 (mt-10) REVERT: E 59 ILE cc_start: 0.8357 (mm) cc_final: 0.7636 (tp) REVERT: M 205 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8239 (mp10) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.3833 time to fit residues: 127.3218 Evaluate side-chains 170 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 262 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 79 optimal weight: 50.0000 chunk 285 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 292 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.113757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073565 restraints weight = 96842.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073171 restraints weight = 70314.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072898 restraints weight = 62560.252| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1237 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1242 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28634 Z= 0.261 Angle : 0.653 9.720 39297 Z= 0.339 Chirality : 0.043 0.264 4671 Planarity : 0.004 0.056 4826 Dihedral : 17.532 179.733 4819 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.89 % Favored : 89.53 % Rotamer: Outliers : 0.08 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -1.05 (0.14), residues: 3458 helix: 1.20 (0.15), residues: 1211 sheet: -0.91 (0.29), residues: 316 loop : -2.02 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1020 HIS 0.012 0.001 HIS C1023 PHE 0.013 0.001 PHE D 172 TYR 0.030 0.001 TYR C1229 ARG 0.009 0.000 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5151.97 seconds wall clock time: 94 minutes 52.91 seconds (5692.91 seconds total)