Starting phenix.real_space_refine on Thu Jul 25 03:35:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/07_2024/6gh6_0002.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/07_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_0002/07_2024/6gh6_0002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/07_2024/6gh6_0002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/07_2024/6gh6_0002.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh6_0002/07_2024/6gh6_0002.cif" } 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-5388/modules/chem_data/mon_lib" Total number of atoms: 28051 Number of models: 1 Model: "" Number of chains: 10 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: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 958 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 139} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "M" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 536 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 35, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 128 Chain: "M" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 381 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 61} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'UNK:plan-1': 16, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 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: 15.24, per 1000 atoms: 0.54 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: 10.70 Conformation dependent library (CDL) restraints added in 4.6 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: 8.67 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 No H-bonds generated for 'chain 'M' and resid 336 through 355' Processing helix chain 'M' and resid 366 through 374 No H-bonds generated for 'chain 'M' and resid 366 through 374' Processing helix chain 'M' and resid 377 through 388 No H-bonds generated for 'chain 'M' and resid 377 through 388' Processing helix chain 'M' and resid 416 through 428 No H-bonds generated for 'chain 'M' and resid 416 through 428' Processing helix chain 'M' and resid 438 through 449 No H-bonds generated for 'chain 'M' and resid 438 through 449' Processing helix chain 'M' and resid 455 through 463 No H-bonds generated for 'chain 'M' and resid 455 through 463' 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 WARNING: can't find one or more strands! previous: chain 'M' and resid 279 through 281 current: chain 'M' and resid 286 through 288 No H-bonds generated for sheet with id=AD9 916 hydrogen bonds defined for protein. 2592 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: 13.22 Time building geometry restraints manager: 11.77 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: 22177 3.12 - 3.71: 41224 3.71 - 4.31: 55747 4.31 - 4.90: 90391 Nonbonded interactions: 209711 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 209706 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 79.640 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.680 ------------------------------------------------------------------------------- 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= 0.277 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 : 3.024 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: 0.4035 time to fit residues: 364.1483 Evaluate side-chains 294 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 40.0000 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 0.2980 chunk 268 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 310 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 28634 Z= 0.367 Angle : 0.753 10.788 39297 Z= 0.396 Chirality : 0.046 0.224 4671 Planarity : 0.005 0.077 4826 Dihedral : 17.811 179.361 4819 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.30 % Favored : 91.12 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % 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: -2.23 (0.13), residues: 3458 helix: -0.66 (0.14), residues: 1154 sheet: -0.73 (0.28), residues: 286 loop : -2.18 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 807 HIS 0.006 0.001 HIS D 104 PHE 0.025 0.002 PHE D 437 TYR 0.044 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 317 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 311 time to evaluate : 3.254 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: A 13 LEU cc_start: 0.9514 (tt) cc_final: 0.9306 (tp) REVERT: A 51 MET cc_start: 0.9292 (mmm) cc_final: 0.8999 (mmm) REVERT: A 97 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8737 (tm-30) REVERT: B 196 THR cc_start: 0.8840 (p) cc_final: 0.8471 (t) REVERT: B 212 ASP cc_start: 0.9150 (t0) cc_final: 0.8791 (t0) REVERT: B 236 ASP cc_start: 0.8583 (t70) cc_final: 0.8121 (p0) REVERT: C 459 MET cc_start: 0.9378 (mtt) cc_final: 0.9134 (mtt) REVERT: C 876 GLU cc_start: 0.9629 (tt0) cc_final: 0.9259 (mp0) REVERT: C 1199 LEU cc_start: 0.9124 (tt) cc_final: 0.8766 (tp) REVERT: C 1319 MET cc_start: 0.8810 (ptp) cc_final: 0.8432 (mtm) REVERT: C 1323 PHE cc_start: 0.9231 (t80) cc_final: 0.8832 (t80) REVERT: D 180 MET cc_start: 0.8318 (tpp) cc_final: 0.8045 (tpt) REVERT: D 339 ARG cc_start: 0.8550 (ttp80) cc_final: 0.7735 (mpt-90) REVERT: D 470 VAL cc_start: 0.9748 (t) cc_final: 0.9367 (p) REVERT: D 500 ILE cc_start: 0.8856 (tt) cc_final: 0.8570 (pt) REVERT: D 641 ILE cc_start: 0.9095 (pt) cc_final: 0.8674 (tp) REVERT: D 701 LEU cc_start: 0.6169 (mt) cc_final: 0.5644 (tp) REVERT: D 743 MET cc_start: 0.8458 (mtp) cc_final: 0.7666 (mmm) REVERT: D 786 THR cc_start: 0.8427 (m) cc_final: 0.7644 (p) REVERT: D 801 VAL cc_start: 0.9749 (t) cc_final: 0.9445 (p) REVERT: D 839 VAL cc_start: 0.9411 (t) cc_final: 0.8991 (p) REVERT: D 901 ARG cc_start: 0.7850 (tpt90) cc_final: 0.7176 (tpm170) REVERT: D 1040 MET cc_start: 0.5207 (mtm) cc_final: 0.4877 (mtt) REVERT: E 5 THR cc_start: 0.9122 (m) cc_final: 0.8767 (t) REVERT: E 53 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9075 (mt-10) REVERT: E 59 ILE cc_start: 0.8594 (mm) cc_final: 0.8037 (tp) REVERT: M 126 TRP cc_start: 0.8949 (t60) cc_final: 0.8726 (t60) REVERT: M 205 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8192 (mp10) outliers start: 6 outliers final: 2 residues processed: 317 average time/residue: 0.4027 time to fit residues: 204.9737 Evaluate side-chains 221 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 277 optimal weight: 40.0000 chunk 308 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 266 ASN D 419 HIS D 792 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 28634 Z= 0.482 Angle : 0.811 10.197 39297 Z= 0.425 Chirality : 0.048 0.290 4671 Planarity : 0.005 0.074 4826 Dihedral : 17.852 177.916 4819 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.63 % Favored : 89.79 % Rotamer: Outliers : 0.23 % Allowed : 4.08 % Favored : 95.70 % 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: -1.85 (0.13), residues: 3458 helix: 0.07 (0.15), residues: 1165 sheet: -1.06 (0.27), residues: 324 loop : -2.16 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 807 HIS 0.016 0.002 HIS C1023 PHE 0.028 0.002 PHE C1270 TYR 0.036 0.003 TYR C1229 ARG 0.011 0.001 ARG D 431 *********************** 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 250 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 2.892 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 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: symmetry clash REVERT: B 212 ASP cc_start: 0.9349 (t0) cc_final: 0.9093 (t0) REVERT: C 459 MET cc_start: 0.9419 (mtt) cc_final: 0.9168 (mtt) REVERT: C 510 GLN cc_start: 0.9188 (pt0) cc_final: 0.8878 (mp10) REVERT: C 876 GLU cc_start: 0.9624 (tt0) cc_final: 0.9169 (mp0) REVERT: C 1199 LEU cc_start: 0.9100 (tt) cc_final: 0.8739 (tp) REVERT: C 1281 TYR cc_start: 0.9074 (m-10) cc_final: 0.8843 (m-10) REVERT: D 180 MET cc_start: 0.8142 (tpp) cc_final: 0.7707 (tpp) REVERT: D 340 GLN cc_start: 0.8969 (tt0) cc_final: 0.8708 (tm-30) REVERT: D 697 MET cc_start: 0.5251 (tpp) cc_final: 0.4927 (tpp) REVERT: D 801 VAL cc_start: 0.9786 (t) cc_final: 0.9544 (p) REVERT: D 839 VAL cc_start: 0.9417 (t) cc_final: 0.9082 (p) REVERT: D 1040 MET cc_start: 0.5003 (mtm) cc_final: 0.4606 (mtt) REVERT: D 1351 VAL cc_start: 0.9262 (t) cc_final: 0.8839 (p) REVERT: E 5 THR cc_start: 0.9244 (m) cc_final: 0.8983 (t) REVERT: E 15 ASN cc_start: 0.8336 (t0) cc_final: 0.7995 (t0) REVERT: E 41 GLU cc_start: 0.8701 (tt0) cc_final: 0.8447 (pp20) REVERT: E 53 GLU cc_start: 0.9597 (mt-10) cc_final: 0.9206 (mt-10) REVERT: E 59 ILE cc_start: 0.8214 (mm) cc_final: 0.7318 (tp) REVERT: M 205 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8305 (mp10) outliers start: 6 outliers final: 5 residues processed: 249 average time/residue: 0.3754 time to fit residues: 152.2445 Evaluate side-chains 192 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 312 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 148 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** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS C1244 HIS C1288 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: 0.7765 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28634 Z= 0.297 Angle : 0.670 10.525 39297 Z= 0.351 Chirality : 0.044 0.214 4671 Planarity : 0.004 0.080 4826 Dihedral : 17.663 175.826 4819 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.53 % Favored : 90.80 % Rotamer: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % 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: -1.46 (0.14), residues: 3458 helix: 0.60 (0.15), residues: 1180 sheet: -0.78 (0.28), residues: 316 loop : -2.11 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 126 HIS 0.007 0.001 HIS C1023 PHE 0.015 0.001 PHE D 172 TYR 0.032 0.002 TYR C1229 ARG 0.008 0.001 ARG C 371 *********************** 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 240 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 2.949 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 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 13 LEU cc_start: 0.9484 (tt) cc_final: 0.9259 (tp) REVERT: B 212 ASP cc_start: 0.9329 (t0) cc_final: 0.9043 (t0) REVERT: B 236 ASP cc_start: 0.8565 (t70) cc_final: 0.8074 (p0) REVERT: C 459 MET cc_start: 0.9405 (mtt) cc_final: 0.9161 (mtt) REVERT: C 510 GLN cc_start: 0.9137 (pt0) cc_final: 0.8821 (mp10) REVERT: C 876 GLU cc_start: 0.9583 (tt0) cc_final: 0.9131 (mp0) REVERT: C 1199 LEU cc_start: 0.9114 (tt) cc_final: 0.8690 (tp) REVERT: D 180 MET cc_start: 0.8047 (tpp) cc_final: 0.7605 (tpp) REVERT: D 801 VAL cc_start: 0.9768 (t) cc_final: 0.9506 (p) REVERT: D 1040 MET cc_start: 0.5013 (mtm) cc_final: 0.4645 (mtt) REVERT: D 1307 LEU cc_start: 0.9288 (mp) cc_final: 0.9053 (mp) REVERT: D 1351 VAL cc_start: 0.9212 (t) cc_final: 0.8714 (p) REVERT: E 5 THR cc_start: 0.9337 (m) cc_final: 0.9002 (t) REVERT: E 41 GLU cc_start: 0.8773 (tt0) cc_final: 0.8504 (pp20) REVERT: E 53 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9150 (mt-10) REVERT: E 59 ILE cc_start: 0.8255 (mm) cc_final: 0.7308 (tp) REVERT: M 205 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8282 (mp10) outliers start: 2 outliers final: 2 residues processed: 240 average time/residue: 0.3659 time to fit residues: 145.3394 Evaluate side-chains 191 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 246 optimal weight: 50.0000 chunk 136 optimal weight: 6.9990 chunk 282 optimal weight: 40.0000 chunk 228 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 83 optimal weight: 40.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- 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** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 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** C 686 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** 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: 0.7785 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28634 Z= 0.358 Angle : 0.710 10.051 39297 Z= 0.370 Chirality : 0.045 0.242 4671 Planarity : 0.005 0.058 4826 Dihedral : 17.640 176.698 4819 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.01 % Favored : 89.33 % Rotamer: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % 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: -1.38 (0.14), residues: 3458 helix: 0.78 (0.15), residues: 1181 sheet: -0.98 (0.29), residues: 310 loop : -2.10 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 126 HIS 0.005 0.001 HIS D 907 PHE 0.018 0.002 PHE C1270 TYR 0.029 0.002 TYR C1229 ARG 0.006 0.001 ARG A 158 *********************** 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 231 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 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 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 212 ASP cc_start: 0.9361 (t0) cc_final: 0.9100 (t0) REVERT: B 236 ASP cc_start: 0.8590 (t70) cc_final: 0.8132 (p0) REVERT: C 459 MET cc_start: 0.9423 (mtt) cc_final: 0.9159 (mtt) REVERT: C 510 GLN cc_start: 0.9112 (pt0) cc_final: 0.8800 (mp10) REVERT: C 876 GLU cc_start: 0.9578 (tt0) cc_final: 0.9175 (mp0) REVERT: C 1095 ASP cc_start: 0.9480 (m-30) cc_final: 0.8870 (m-30) REVERT: C 1199 LEU cc_start: 0.9135 (tt) cc_final: 0.8727 (tp) REVERT: D 180 MET cc_start: 0.8137 (tpp) cc_final: 0.7785 (tpp) REVERT: D 743 MET cc_start: 0.8437 (tpp) cc_final: 0.8041 (tpp) REVERT: D 801 VAL cc_start: 0.9777 (t) cc_final: 0.9526 (p) REVERT: D 839 VAL cc_start: 0.9368 (t) cc_final: 0.8982 (p) REVERT: D 1040 MET cc_start: 0.5071 (mtm) cc_final: 0.4710 (mtt) REVERT: D 1351 VAL cc_start: 0.9297 (t) cc_final: 0.8799 (p) REVERT: E 5 THR cc_start: 0.9240 (m) cc_final: 0.8898 (t) REVERT: E 11 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8970 (mm-30) REVERT: E 41 GLU cc_start: 0.8585 (tt0) cc_final: 0.8329 (pp20) REVERT: E 53 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9312 (mt-10) REVERT: E 59 ILE cc_start: 0.8222 (mm) cc_final: 0.7364 (tp) REVERT: M 205 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8306 (mp10) outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.3649 time to fit residues: 139.1610 Evaluate side-chains 187 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 1.9990 chunk 297 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 81 optimal weight: 0.0980 chunk 330 optimal weight: 8.9990 chunk 274 optimal weight: 10.0000 chunk 153 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 GLN ** C 437 ASN ** 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** D 897 HIS ** 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: 0.7736 moved from start: 0.5306 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= 0.186 Angle : 0.615 9.829 39297 Z= 0.320 Chirality : 0.043 0.213 4671 Planarity : 0.004 0.052 4826 Dihedral : 17.477 177.592 4819 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.65 % Favored : 90.78 % Rotamer: Outliers : 0.08 % Allowed : 1.26 % Favored : 98.67 % 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: -1.07 (0.14), residues: 3458 helix: 1.15 (0.16), residues: 1181 sheet: -0.70 (0.29), residues: 306 loop : -2.00 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 126 HIS 0.005 0.001 HIS D 907 PHE 0.012 0.001 PHE D 172 TYR 0.022 0.001 TYR C1149 ARG 0.007 0.000 ARG A 158 *********************** 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 246 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 2.910 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: A 13 LEU cc_start: 0.9453 (tt) cc_final: 0.9230 (tp) REVERT: A 152 TYR cc_start: 0.8644 (t80) cc_final: 0.8400 (t80) REVERT: B 29 GLU cc_start: 0.9620 (tt0) cc_final: 0.9308 (tm-30) REVERT: B 212 ASP cc_start: 0.9328 (t0) cc_final: 0.9059 (t0) REVERT: B 236 ASP cc_start: 0.8593 (t70) cc_final: 0.8129 (p0) REVERT: C 459 MET cc_start: 0.9400 (mtt) cc_final: 0.9136 (mtt) REVERT: C 510 GLN cc_start: 0.9053 (pt0) cc_final: 0.8777 (mp10) REVERT: C 876 GLU cc_start: 0.9532 (tt0) cc_final: 0.9174 (mp0) REVERT: C 1095 ASP cc_start: 0.9457 (m-30) cc_final: 0.8873 (m-30) REVERT: C 1131 MET cc_start: 0.9266 (ttm) cc_final: 0.9014 (ttm) REVERT: C 1199 LEU cc_start: 0.9111 (tt) cc_final: 0.8668 (tp) REVERT: D 180 MET cc_start: 0.8113 (tpp) cc_final: 0.7825 (tpp) REVERT: D 743 MET cc_start: 0.8423 (tpp) cc_final: 0.8031 (tpp) REVERT: D 801 VAL cc_start: 0.9755 (t) cc_final: 0.9485 (p) REVERT: D 839 VAL cc_start: 0.9396 (t) cc_final: 0.9006 (p) REVERT: D 1040 MET cc_start: 0.5043 (mtm) cc_final: 0.4654 (mtt) REVERT: D 1260 MET cc_start: 0.8993 (tpp) cc_final: 0.8504 (tmm) REVERT: D 1351 VAL cc_start: 0.9265 (t) cc_final: 0.8733 (p) REVERT: E 5 THR cc_start: 0.9208 (m) cc_final: 0.8896 (t) REVERT: E 53 GLU cc_start: 0.9644 (mt-10) cc_final: 0.9215 (mt-10) REVERT: E 59 ILE cc_start: 0.8293 (mm) cc_final: 0.7430 (tp) REVERT: M 205 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8229 (mp10) outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.3776 time to fit residues: 152.0803 Evaluate side-chains 195 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 188 optimal weight: 20.0000 chunk 241 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 278 optimal weight: 0.4980 chunk 184 optimal weight: 50.0000 chunk 329 optimal weight: 40.0000 chunk 206 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN D 335 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5695 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= 0.340 Angle : 0.693 10.847 39297 Z= 0.359 Chirality : 0.044 0.265 4671 Planarity : 0.004 0.057 4826 Dihedral : 17.580 178.275 4819 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.18 % Favored : 89.24 % Rotamer: Outliers : 0.04 % Allowed : 1.71 % Favored : 98.25 % 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: 1182 sheet: -0.95 (0.29), residues: 315 loop : -2.00 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D1020 HIS 0.006 0.001 HIS D 907 PHE 0.014 0.002 PHE D 172 TYR 0.023 0.002 TYR D 360 ARG 0.008 0.000 ARG A 158 *********************** 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 220 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 3.149 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.9420 (mtt) cc_final: 0.9138 (mtt) REVERT: C 510 GLN cc_start: 0.9190 (pt0) cc_final: 0.8895 (mp10) REVERT: C 876 GLU cc_start: 0.9601 (tt0) cc_final: 0.9216 (mp0) REVERT: C 1095 ASP cc_start: 0.9437 (m-30) cc_final: 0.8863 (m-30) REVERT: C 1199 LEU cc_start: 0.9153 (tt) cc_final: 0.8760 (tp) REVERT: D 180 MET cc_start: 0.8125 (tpp) cc_final: 0.7888 (tpp) REVERT: D 743 MET cc_start: 0.8425 (tpp) cc_final: 0.7894 (tpp) REVERT: D 801 VAL cc_start: 0.9778 (t) cc_final: 0.9519 (p) REVERT: D 839 VAL cc_start: 0.9381 (t) cc_final: 0.9015 (p) REVERT: D 1040 MET cc_start: 0.5057 (mtm) cc_final: 0.4703 (mtt) REVERT: D 1260 MET cc_start: 0.9051 (tpp) cc_final: 0.8562 (mmm) REVERT: D 1351 VAL cc_start: 0.9280 (t) cc_final: 0.8817 (p) REVERT: E 5 THR cc_start: 0.9142 (m) cc_final: 0.8802 (t) REVERT: E 53 GLU cc_start: 0.9631 (mt-10) cc_final: 0.9228 (mt-10) REVERT: E 59 ILE cc_start: 0.8188 (mm) cc_final: 0.7363 (tp) REVERT: M 205 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8296 (mp10) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.3835 time to fit residues: 140.2788 Evaluate side-chains 186 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 196 optimal weight: 50.0000 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 224 optimal weight: 0.0270 chunk 162 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN E 15 ASN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 28634 Z= 0.434 Angle : 0.754 10.143 39297 Z= 0.392 Chirality : 0.046 0.321 4671 Planarity : 0.005 0.062 4826 Dihedral : 17.825 179.556 4819 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.61 % Favored : 88.78 % Rotamer: Outliers : 0.08 % Allowed : 1.75 % Favored : 98.17 % 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: -1.37 (0.14), residues: 3458 helix: 0.84 (0.15), residues: 1203 sheet: -1.18 (0.28), residues: 326 loop : -2.11 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D1020 HIS 0.006 0.001 HIS D 907 PHE 0.028 0.002 PHE C 506 TYR 0.027 0.002 TYR D 360 ARG 0.007 0.001 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 211 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 3.107 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: B 29 GLU cc_start: 0.9658 (tt0) cc_final: 0.9410 (tm-30) REVERT: C 459 MET cc_start: 0.9438 (mtt) cc_final: 0.9151 (mtt) REVERT: C 510 GLN cc_start: 0.9240 (pt0) cc_final: 0.8957 (mp10) REVERT: C 876 GLU cc_start: 0.9591 (tt0) cc_final: 0.9185 (mp0) REVERT: C 1095 ASP cc_start: 0.9435 (m-30) cc_final: 0.8843 (m-30) REVERT: C 1199 LEU cc_start: 0.9177 (tt) cc_final: 0.8885 (tp) REVERT: D 102 MET cc_start: 0.9044 (ptp) cc_final: 0.8839 (pmm) REVERT: D 801 VAL cc_start: 0.9780 (t) cc_final: 0.9553 (p) REVERT: D 1040 MET cc_start: 0.5018 (mtm) cc_final: 0.4651 (mtt) REVERT: D 1260 MET cc_start: 0.9105 (tpp) cc_final: 0.8470 (mmm) REVERT: E 5 THR cc_start: 0.9089 (m) cc_final: 0.8758 (t) REVERT: E 53 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9182 (mt-10) REVERT: E 59 ILE cc_start: 0.8062 (mm) cc_final: 0.7022 (tp) REVERT: M 205 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8319 (mp10) outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.3747 time to fit residues: 132.2835 Evaluate side-chains 176 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 288 optimal weight: 7.9990 chunk 307 optimal weight: 4.9990 chunk 184 optimal weight: 30.0000 chunk 133 optimal weight: 0.9990 chunk 241 optimal weight: 0.9980 chunk 94 optimal weight: 0.0370 chunk 277 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 23 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN ** 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: 0.7737 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28634 Z= 0.182 Angle : 0.632 10.886 39297 Z= 0.325 Chirality : 0.043 0.290 4671 Planarity : 0.004 0.052 4826 Dihedral : 17.561 178.900 4819 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.14 % Favored : 90.23 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % 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: -1.07 (0.14), residues: 3458 helix: 1.22 (0.15), residues: 1196 sheet: -0.92 (0.28), residues: 326 loop : -2.04 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1020 HIS 0.007 0.001 HIS D 907 PHE 0.016 0.001 PHE C 828 TYR 0.032 0.001 TYR D 360 ARG 0.008 0.000 ARG E 67 *********************** 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 221 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.944 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 29 GLU cc_start: 0.9618 (tt0) cc_final: 0.9312 (tm-30) REVERT: C 459 MET cc_start: 0.9420 (mtt) cc_final: 0.9156 (mtt) REVERT: C 510 GLN cc_start: 0.9109 (pt0) cc_final: 0.8842 (mp10) REVERT: C 876 GLU cc_start: 0.9540 (tt0) cc_final: 0.9160 (mp0) REVERT: C 1095 ASP cc_start: 0.9430 (m-30) cc_final: 0.8866 (m-30) REVERT: C 1199 LEU cc_start: 0.9126 (tt) cc_final: 0.8868 (tp) REVERT: C 1232 MET cc_start: 0.9074 (mtp) cc_final: 0.8706 (mtp) REVERT: D 102 MET cc_start: 0.9051 (ptp) cc_final: 0.8848 (pmm) REVERT: D 743 MET cc_start: 0.8355 (tpp) cc_final: 0.7938 (tpp) REVERT: D 744 ARG cc_start: 0.8250 (tpt170) cc_final: 0.8049 (tpp80) REVERT: D 801 VAL cc_start: 0.9756 (t) cc_final: 0.9488 (p) REVERT: D 839 VAL cc_start: 0.9334 (t) cc_final: 0.8930 (p) REVERT: D 1040 MET cc_start: 0.4941 (mtm) cc_final: 0.4576 (mtt) REVERT: D 1260 MET cc_start: 0.9065 (tpp) cc_final: 0.8474 (mmm) REVERT: D 1306 LEU cc_start: 0.9340 (tp) cc_final: 0.8715 (tp) REVERT: D 1351 VAL cc_start: 0.9353 (t) cc_final: 0.8885 (p) REVERT: E 5 THR cc_start: 0.9045 (m) cc_final: 0.8638 (p) REVERT: M 205 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8275 (mp10) outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.4833 time to fit residues: 179.2488 Evaluate side-chains 180 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 7.9990 chunk 324 optimal weight: 40.0000 chunk 198 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 chunk 313 optimal weight: 0.0060 chunk 271 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 209 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28634 Z= 0.178 Angle : 0.619 10.932 39297 Z= 0.318 Chirality : 0.042 0.275 4671 Planarity : 0.004 0.071 4826 Dihedral : 17.388 178.309 4819 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.20 % Favored : 90.17 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.77 % 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: -0.98 (0.15), residues: 3458 helix: 1.29 (0.15), residues: 1204 sheet: -0.71 (0.30), residues: 303 loop : -2.01 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1020 HIS 0.006 0.001 HIS D 907 PHE 0.011 0.001 PHE D 172 TYR 0.029 0.001 TYR D 360 ARG 0.009 0.000 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 221 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 3.346 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.9609 (tt0) cc_final: 0.9299 (tm-30) REVERT: C 459 MET cc_start: 0.9430 (mtt) cc_final: 0.9142 (mtt) REVERT: C 510 GLN cc_start: 0.9086 (pt0) cc_final: 0.8827 (mp10) REVERT: C 876 GLU cc_start: 0.9538 (tt0) cc_final: 0.9145 (mp0) REVERT: C 1095 ASP cc_start: 0.9429 (m-30) cc_final: 0.8870 (m-30) REVERT: C 1199 LEU cc_start: 0.9120 (tt) cc_final: 0.8890 (tp) REVERT: C 1232 MET cc_start: 0.9070 (mtp) cc_final: 0.8707 (mtp) REVERT: D 743 MET cc_start: 0.8388 (tpp) cc_final: 0.7888 (tpp) REVERT: D 801 VAL cc_start: 0.9761 (t) cc_final: 0.9495 (p) REVERT: D 839 VAL cc_start: 0.9349 (t) cc_final: 0.8956 (p) REVERT: D 1040 MET cc_start: 0.5181 (mtm) cc_final: 0.4800 (mtt) REVERT: D 1260 MET cc_start: 0.9071 (tpp) cc_final: 0.8808 (mmm) REVERT: D 1306 LEU cc_start: 0.9351 (tp) cc_final: 0.8983 (tp) REVERT: E 5 THR cc_start: 0.9052 (m) cc_final: 0.8661 (p) REVERT: E 59 ILE cc_start: 0.7937 (mm) cc_final: 0.7065 (tp) REVERT: M 205 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8241 (mp10) outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.3647 time to fit residues: 133.4765 Evaluate side-chains 180 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.112464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072460 restraints weight = 97136.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071887 restraints weight = 71240.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.071378 restraints weight = 68590.693| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1237 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1238 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28634 Z= 0.361 Angle : 0.707 10.316 39297 Z= 0.366 Chirality : 0.045 0.284 4671 Planarity : 0.004 0.067 4826 Dihedral : 17.558 178.715 4819 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.38 % Favored : 88.95 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.77 % 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: -1.12 (0.14), residues: 3458 helix: 1.13 (0.15), residues: 1200 sheet: -1.05 (0.28), residues: 327 loop : -2.03 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1020 HIS 0.007 0.001 HIS D 907 PHE 0.020 0.002 PHE C 828 TYR 0.022 0.002 TYR C 810 ARG 0.009 0.001 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4973.87 seconds wall clock time: 89 minutes 43.44 seconds (5383.44 seconds total)