Starting phenix.real_space_refine on Sun Sep 29 03:25:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/09_2024/7zkp_14764.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/09_2024/7zkp_14764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/09_2024/7zkp_14764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/09_2024/7zkp_14764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/09_2024/7zkp_14764.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/09_2024/7zkp_14764.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.099 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 8 5.49 5 S 80 5.16 5 C 13161 2.51 5 N 3145 2.21 5 O 3535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19929 Number of models: 1 Model: "" Number of chains: 19 Chain: "D" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "L" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "X" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1274 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "1" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2426 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 290} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3776 Classifications: {'peptide': 469} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 461} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 909 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "6" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "9" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2763 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1749 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "b" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 11.69, per 1000 atoms: 0.59 Number of scatterers: 19929 At special positions: 0 Unit cell: (129.171, 118.307, 150.901, 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 80 16.00 P 8 15.00 O 3535 8.00 N 3145 7.00 C 13161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.03 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.04 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.04 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 5.67 Conformation dependent library (CDL) restraints added in 2.5 seconds 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4630 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 5 sheets defined 69.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'D' and resid 4 through 34 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 43 through 58 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'L' and resid 2 through 19 Processing helix chain 'L' and resid 21 through 48 Processing helix chain 'L' and resid 49 through 79 removed outlier: 4.447A pdb=" N SER L 53 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 61 removed outlier: 5.235A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE U 41 " --> pdb=" O SER U 37 " (cutoff:3.500A) Proline residue: U 48 - end of helix removed outlier: 3.682A pdb=" N GLN U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 68 Processing helix chain 'U' and resid 68 through 90 removed outlier: 3.558A pdb=" N GLY U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 104 Processing helix chain 'U' and resid 107 through 110 removed outlier: 3.515A pdb=" N GLY U 110 " --> pdb=" O GLN U 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 107 through 110' Processing helix chain 'U' and resid 111 through 126 Processing helix chain 'U' and resid 141 through 145 Processing helix chain 'U' and resid 156 through 170 Processing helix chain 'W' and resid 32 through 96 removed outlier: 3.527A pdb=" N LEU W 69 " --> pdb=" O ALA W 65 " (cutoff:3.500A) Proline residue: W 71 - end of helix Processing helix chain 'X' and resid 27 through 34 Processing helix chain 'X' and resid 36 through 61 Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 71 through 99 Processing helix chain 'X' and resid 104 through 122 Processing helix chain 'X' and resid 132 through 144 Processing helix chain 'X' and resid 145 through 150 Processing helix chain '1' and resid 2 through 34 removed outlier: 3.766A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 58 removed outlier: 4.217A pdb=" N GLN 1 49 " --> pdb=" O TYR 1 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA 1 52 " --> pdb=" O LEU 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 87 Proline residue: 1 77 - end of helix Processing helix chain '1' and resid 104 through 116 Processing helix chain '1' and resid 117 through 127 removed outlier: 3.802A pdb=" N LEU 1 121 " --> pdb=" O VAL 1 117 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER 1 127 " --> pdb=" O SER 1 123 " (cutoff:3.500A) Processing helix chain '1' and resid 129 through 159 removed outlier: 3.706A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 173 Processing helix chain '1' and resid 182 through 197 removed outlier: 3.692A pdb=" N THR 1 197 " --> pdb=" O SER 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 223 through 246 Processing helix chain '1' and resid 255 through 263 Processing helix chain '1' and resid 267 through 298 Processing helix chain '1' and resid 304 through 315 removed outlier: 3.645A pdb=" N CYS 1 312 " --> pdb=" O LEU 1 308 " (cutoff:3.500A) Processing helix chain '1' and resid 315 through 334 removed outlier: 3.714A pdb=" N LEU 1 319 " --> pdb=" O ILE 1 315 " (cutoff:3.500A) Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 2 through 15 removed outlier: 3.589A pdb=" N MET 2 15 " --> pdb=" O THR 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 19 No H-bonds generated for 'chain '2' and resid 17 through 19' Processing helix chain '2' and resid 20 through 39 Processing helix chain '2' and resid 40 through 50 removed outlier: 3.957A pdb=" N LEU 2 47 " --> pdb=" O LEU 2 44 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN 2 48 " --> pdb=" O LEU 2 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN 2 49 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 85 Processing helix chain '2' and resid 90 through 97 Processing helix chain '2' and resid 102 through 119 Processing helix chain '2' and resid 122 through 143 Processing helix chain '2' and resid 147 through 180 removed outlier: 3.565A pdb=" N ALA 2 153 " --> pdb=" O LYS 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 183 through 187 removed outlier: 3.947A pdb=" N SER 2 186 " --> pdb=" O THR 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 195 Processing helix chain '2' and resid 197 through 213 removed outlier: 3.793A pdb=" N ILE 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 228 Processing helix chain '2' and resid 229 through 237 removed outlier: 4.356A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 238 through 252 Processing helix chain '2' and resid 257 through 277 removed outlier: 3.729A pdb=" N LEU 2 276 " --> pdb=" O SER 2 272 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU 2 277 " --> pdb=" O VAL 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 280 through 298 Processing helix chain '2' and resid 299 through 302 removed outlier: 3.812A pdb=" N LEU 2 302 " --> pdb=" O LEU 2 299 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 299 through 302' Processing helix chain '2' and resid 305 through 330 Processing helix chain '2' and resid 331 through 334 removed outlier: 3.535A pdb=" N ILE 2 334 " --> pdb=" O ILE 2 331 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 331 through 334' Processing helix chain '2' and resid 346 through 351 Processing helix chain '2' and resid 352 through 356 Processing helix chain '2' and resid 357 through 373 Processing helix chain '2' and resid 377 through 393 removed outlier: 3.559A pdb=" N PHE 2 381 " --> pdb=" O LEU 2 377 " (cutoff:3.500A) Processing helix chain '2' and resid 395 through 421 removed outlier: 3.786A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 436 through 453 Processing helix chain '2' and resid 456 through 468 Processing helix chain '3' and resid 3 through 25 Proline residue: 3 12 - end of helix removed outlier: 4.233A pdb=" N LEU 3 25 " --> pdb=" O VAL 3 21 " (cutoff:3.500A) Processing helix chain '3' and resid 53 through 72 removed outlier: 3.641A pdb=" N ILE 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix Processing helix chain '3' and resid 73 through 79 removed outlier: 3.538A pdb=" N SER 3 79 " --> pdb=" O PRO 3 75 " (cutoff:3.500A) Processing helix chain '3' and resid 83 through 108 removed outlier: 3.514A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 7 removed outlier: 3.688A pdb=" N TYR 6 7 " --> pdb=" O TYR 6 3 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 25 Processing helix chain '6' and resid 28 through 51 removed outlier: 3.512A pdb=" N SER 6 32 " --> pdb=" O ASN 6 28 " (cutoff:3.500A) Processing helix chain '6' and resid 52 through 66 removed outlier: 3.724A pdb=" N ILE 6 64 " --> pdb=" O ILE 6 60 " (cutoff:3.500A) Processing helix chain '6' and resid 66 through 81 removed outlier: 4.661A pdb=" N ASN 6 81 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 92 removed outlier: 3.994A pdb=" N ARG 6 92 " --> pdb=" O SER 6 89 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 89 through 92' Processing helix chain '6' and resid 93 through 110 Processing helix chain '6' and resid 111 through 117 Processing helix chain '6' and resid 118 through 128 removed outlier: 3.824A pdb=" N LEU 6 122 " --> pdb=" O LEU 6 118 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN 6 128 " --> pdb=" O GLU 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 156 Processing helix chain '6' and resid 158 through 181 Proline residue: 6 176 - end of helix Processing helix chain 'g' and resid 11 through 23 Processing helix chain 'g' and resid 23 through 51 removed outlier: 3.605A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Proline residue: g 45 - end of helix Processing helix chain 'b' and resid 3 through 25 Processing helix chain 'b' and resid 32 through 64 removed outlier: 3.790A pdb=" N LYS b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain '9' and resid 15 through 29 Processing helix chain '9' and resid 31 through 36 removed outlier: 4.345A pdb=" N ALA 9 35 " --> pdb=" O LYS 9 32 " (cutoff:3.500A) Processing helix chain '9' and resid 37 through 50 Processing helix chain '9' and resid 50 through 66 Processing helix chain '9' and resid 80 through 84 removed outlier: 3.615A pdb=" N ILE 9 84 " --> pdb=" O VAL 9 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 removed outlier: 3.905A pdb=" N ALA C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 522 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 538 removed outlier: 3.600A pdb=" N THR C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET C 534 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 535 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 Processing helix chain 'C' and resid 555 through 565 removed outlier: 3.564A pdb=" N TYR C 565 " --> pdb=" O HIS C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 removed outlier: 3.873A pdb=" N GLU C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 600 removed outlier: 4.025A pdb=" N LYS C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 623 Processing helix chain 'C' and resid 630 through 642 removed outlier: 4.473A pdb=" N VAL C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 659 removed outlier: 3.566A pdb=" N ILE C 650 " --> pdb=" O TYR C 646 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 651 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 680 removed outlier: 3.595A pdb=" N VAL C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 695 removed outlier: 3.522A pdb=" N GLN C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 714 Processing helix chain 'C' and resid 717 through 732 Proline residue: C 729 - end of helix Processing helix chain 'C' and resid 736 through 750 removed outlier: 3.886A pdb=" N GLN C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 743 " --> pdb=" O ASN C 739 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 767 removed outlier: 3.578A pdb=" N LEU C 757 " --> pdb=" O TYR C 753 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 758 " --> pdb=" O ARG C 754 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 removed outlier: 3.797A pdb=" N ALA C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 800 removed outlier: 3.582A pdb=" N GLU C 793 " --> pdb=" O LYS C 789 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP C 795 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 798 " --> pdb=" O GLN C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 809 removed outlier: 3.653A pdb=" N LEU C 805 " --> pdb=" O PRO C 801 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 806 " --> pdb=" O GLU C 802 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 807 " --> pdb=" O MET C 803 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 808 " --> pdb=" O TRP C 804 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 842 removed outlier: 3.540A pdb=" N GLU C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing sheet with id=AA1, first strand: chain '6' and resid 132 through 134 removed outlier: 3.639A pdb=" N TRP D 80 " --> pdb=" O PHE U 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.412A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 61 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 45 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.412A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE A 192 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG A 111 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 194 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 34 removed outlier: 5.426A pdb=" N VAL A 176 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A 123 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 130 " --> pdb=" O SER A 123 " (cutoff:3.500A) 1235 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3068 1.31 - 1.44: 5542 1.44 - 1.57: 11617 1.57 - 1.70: 20 1.70 - 1.84: 134 Bond restraints: 20381 Sorted by residual: bond pdb=" C LEU X 131 " pdb=" O LEU X 131 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.17e-02 7.31e+03 2.46e+01 bond pdb=" CB PLC 1 401 " pdb=" O3 PLC 1 401 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C11 CPL 2 501 " pdb=" O3 CPL 2 501 " ideal model delta sigma weight residual 1.327 1.417 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C' PLC 1 401 " pdb=" O2 PLC 1 401 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta sigma weight residual 1.532 1.455 0.078 1.79e-02 3.12e+03 1.89e+01 ... (remaining 20376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 27546 5.00 - 10.00: 64 10.00 - 15.00: 3 15.00 - 20.00: 3 20.00 - 25.00: 1 Bond angle restraints: 27617 Sorted by residual: angle pdb=" C39 CPL 2 501 " pdb=" C40 CPL 2 501 " pdb=" C41 CPL 2 501 " ideal model delta sigma weight residual 127.51 152.51 -25.00 3.00e+00 1.11e-01 6.94e+01 angle pdb=" C38 CPL 2 501 " pdb=" C39 CPL 2 501 " pdb=" C40 CPL 2 501 " ideal model delta sigma weight residual 127.82 111.74 16.08 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3P PLC 1 401 " pdb=" P PLC 1 401 " pdb=" O4P PLC 1 401 " ideal model delta sigma weight residual 93.62 109.53 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" N ILE 3 23 " pdb=" CA ILE 3 23 " pdb=" C ILE 3 23 " ideal model delta sigma weight residual 113.07 105.90 7.17 1.36e+00 5.41e-01 2.78e+01 angle pdb=" O3P CPL 2 501 " pdb=" P CPL 2 501 " pdb=" O4P CPL 2 501 " ideal model delta sigma weight residual 93.29 108.55 -15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 27612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 11876 35.63 - 71.26: 275 71.26 - 106.89: 22 106.89 - 142.52: 3 142.52 - 178.15: 3 Dihedral angle restraints: 12179 sinusoidal: 4981 harmonic: 7198 Sorted by residual: dihedral pdb=" N SER X 130 " pdb=" C SER X 130 " pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta harmonic sigma weight residual 122.80 109.23 13.57 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" N CPL 2 501 " pdb=" C4 CPL 2 501 " pdb=" C5 CPL 2 501 " pdb=" O4P CPL 2 501 " ideal model delta sinusoidal sigma weight residual 288.92 110.77 178.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C SER X 130 " pdb=" N SER X 130 " pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta harmonic sigma weight residual -122.60 -111.24 -11.36 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 12176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2602 0.054 - 0.107: 520 0.107 - 0.161: 43 0.161 - 0.214: 10 0.214 - 0.268: 3 Chirality restraints: 3178 Sorted by residual: chirality pdb=" CA THR X 128 " pdb=" N THR X 128 " pdb=" C THR X 128 " pdb=" CB THR X 128 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA SER X 130 " pdb=" N SER X 130 " pdb=" C SER X 130 " pdb=" CB SER X 130 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 PLC 1 401 " pdb=" C1 PLC 1 401 " pdb=" C3 PLC 1 401 " pdb=" O2 PLC 1 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.53 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 3175 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 23 " 0.077 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 24 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 804 " 0.021 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP C 804 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 804 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 804 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 804 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 804 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 804 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 804 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 804 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 804 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY X 127 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C GLY X 127 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY X 127 " -0.015 2.00e-02 2.50e+03 pdb=" N THR X 128 " -0.013 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 299 2.68 - 3.23: 19830 3.23 - 3.79: 32234 3.79 - 4.34: 43544 4.34 - 4.90: 70695 Nonbonded interactions: 166602 Sorted by model distance: nonbonded pdb=" O PHE X 151 " pdb=" OH TYR 2 73 " model vdw 2.119 3.040 nonbonded pdb=" OD1 ASP A 130 " pdb=" ND2 ASN A 158 " model vdw 2.137 3.120 nonbonded pdb=" NH2 ARG X 30 " pdb=" OD1 ASP X 111 " model vdw 2.146 3.120 nonbonded pdb=" NH1 ARG X 30 " pdb=" OE1 GLN X 114 " model vdw 2.166 3.120 nonbonded pdb=" O ILE 2 10 " pdb=" OG SER 2 14 " model vdw 2.170 3.040 ... (remaining 166597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.870 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 0.091 20381 Z= 0.287 Angle : 0.731 25.001 27617 Z= 0.368 Chirality : 0.042 0.268 3178 Planarity : 0.005 0.115 3396 Dihedral : 15.303 178.146 7531 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2413 helix: 1.43 (0.13), residues: 1549 sheet: -1.27 (0.62), residues: 70 loop : -0.65 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 804 HIS 0.006 0.001 HIS 2 320 PHE 0.036 0.001 PHE L 26 TYR 0.020 0.001 TYR 2 157 ARG 0.005 0.000 ARG X 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 603 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 53 ASP cc_start: 0.4954 (m-30) cc_final: 0.4530 (m-30) REVERT: U 13 GLU cc_start: 0.6464 (tt0) cc_final: 0.5518 (tt0) REVERT: U 143 PHE cc_start: 0.6303 (p90) cc_final: 0.5926 (p90) REVERT: U 144 LEU cc_start: 0.7778 (mt) cc_final: 0.7450 (mt) REVERT: W 43 TYR cc_start: 0.7405 (t80) cc_final: 0.7069 (t80) REVERT: X 19 TYR cc_start: 0.6414 (m-80) cc_final: 0.6141 (m-10) REVERT: X 107 GLU cc_start: 0.7125 (mp0) cc_final: 0.6481 (mp0) REVERT: X 109 LYS cc_start: 0.7600 (tppt) cc_final: 0.6995 (mtmt) REVERT: X 112 GLU cc_start: 0.6711 (tt0) cc_final: 0.6498 (tm-30) REVERT: X 124 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8014 (mm-30) REVERT: 1 30 LEU cc_start: 0.7058 (mt) cc_final: 0.6782 (mt) REVERT: 1 139 SER cc_start: 0.8359 (t) cc_final: 0.8106 (t) REVERT: 2 188 ASP cc_start: 0.6135 (m-30) cc_final: 0.5795 (t70) REVERT: 6 137 ASP cc_start: 0.7605 (p0) cc_final: 0.7386 (p0) REVERT: b 36 TYR cc_start: 0.7828 (m-80) cc_final: 0.7254 (m-80) REVERT: C 801 PRO cc_start: 0.6843 (Cg_endo) cc_final: 0.6521 (Cg_exo) REVERT: C 804 TRP cc_start: 0.7246 (t60) cc_final: 0.6830 (t60) REVERT: A 175 THR cc_start: 0.7804 (p) cc_final: 0.7035 (t) outliers start: 2 outliers final: 0 residues processed: 605 average time/residue: 0.3417 time to fit residues: 306.6170 Evaluate side-chains 306 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS D 78 HIS U 8 HIS U 119 ASN X 145 HIS 1 69 ASN 1 310 ASN 2 29 ASN 2 198 ASN 3 53 ASN 3 85 ASN 3 107 ASN C 583 HIS ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN A 72 ASN A 88 GLN A 134 HIS A 165 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20381 Z= 0.380 Angle : 0.760 10.794 27617 Z= 0.388 Chirality : 0.046 0.362 3178 Planarity : 0.005 0.080 3396 Dihedral : 12.261 150.684 2979 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.64 % Favored : 95.19 % Rotamer: Outliers : 2.76 % Allowed : 11.05 % Favored : 86.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2413 helix: 1.37 (0.13), residues: 1557 sheet: -1.19 (0.56), residues: 85 loop : -0.72 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 804 HIS 0.009 0.002 HIS g 55 PHE 0.028 0.002 PHE C 599 TYR 0.027 0.002 TYR 1 244 ARG 0.013 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 303 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7349 (ttp) REVERT: D 46 ASP cc_start: 0.6715 (m-30) cc_final: 0.5984 (m-30) REVERT: U 18 MET cc_start: 0.6890 (tpt) cc_final: 0.6655 (tpt) REVERT: U 59 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: W 88 GLN cc_start: 0.6178 (tp40) cc_final: 0.5738 (tt0) REVERT: W 119 MET cc_start: 0.6881 (ptm) cc_final: 0.6659 (ptm) REVERT: X 19 TYR cc_start: 0.8062 (m-80) cc_final: 0.7846 (m-80) REVERT: X 23 ASP cc_start: 0.7922 (t0) cc_final: 0.7313 (t0) REVERT: X 107 GLU cc_start: 0.7491 (mp0) cc_final: 0.6921 (mp0) REVERT: X 109 LYS cc_start: 0.8056 (tppt) cc_final: 0.7418 (mttt) REVERT: X 124 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8076 (mm-30) REVERT: 1 21 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.6109 (t80) REVERT: 1 139 SER cc_start: 0.8164 (t) cc_final: 0.7592 (p) REVERT: 2 63 SER cc_start: 0.8609 (p) cc_final: 0.8364 (p) REVERT: 2 179 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8813 (mt) REVERT: 2 188 ASP cc_start: 0.6277 (m-30) cc_final: 0.5957 (t70) REVERT: 6 2 MET cc_start: 0.2847 (mmm) cc_final: 0.2624 (mmm) REVERT: 6 90 ASN cc_start: 0.6936 (p0) cc_final: 0.6529 (p0) REVERT: 6 137 ASP cc_start: 0.8216 (p0) cc_final: 0.7981 (p0) REVERT: g 30 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.7061 (t80) REVERT: 9 25 CYS cc_start: 0.4606 (t) cc_final: 0.4025 (t) REVERT: C 533 PHE cc_start: 0.7569 (t80) cc_final: 0.7097 (t80) REVERT: C 570 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6245 (tm-30) REVERT: A 84 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8308 (mtm180) REVERT: A 196 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7347 (ptpt) outliers start: 59 outliers final: 28 residues processed: 340 average time/residue: 0.3186 time to fit residues: 168.7211 Evaluate side-chains 287 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 330 THR Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 29 ASN Chi-restraints excluded: chain 2 residue 116 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 330 SER Chi-restraints excluded: chain 2 residue 374 ILE Chi-restraints excluded: chain 6 residue 36 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 88 LYS Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain 9 residue 64 LEU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 196 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 179 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 73 optimal weight: 0.5980 chunk 173 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN U 106 HIS W 114 HIS ** b 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN A 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20381 Z= 0.286 Angle : 0.607 9.030 27617 Z= 0.310 Chirality : 0.041 0.173 3178 Planarity : 0.004 0.066 3396 Dihedral : 11.652 160.101 2979 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 2.44 % Allowed : 13.96 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2413 helix: 1.65 (0.13), residues: 1566 sheet: -1.15 (0.54), residues: 87 loop : -0.65 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP U 149 HIS 0.006 0.001 HIS C 583 PHE 0.025 0.002 PHE C 530 TYR 0.020 0.002 TYR A 117 ARG 0.039 0.001 ARG W 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 275 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.6957 (m-30) cc_final: 0.6086 (m-30) REVERT: U 59 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: W 119 MET cc_start: 0.7178 (ptm) cc_final: 0.6874 (ptm) REVERT: X 19 TYR cc_start: 0.8239 (m-80) cc_final: 0.7977 (m-80) REVERT: X 23 ASP cc_start: 0.7916 (t0) cc_final: 0.7407 (t0) REVERT: X 109 LYS cc_start: 0.8145 (tppt) cc_final: 0.7541 (mtmt) REVERT: X 111 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7235 (t0) REVERT: X 124 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7952 (mm-30) REVERT: 1 139 SER cc_start: 0.8360 (t) cc_final: 0.7831 (p) REVERT: 1 273 PHE cc_start: 0.6332 (t80) cc_final: 0.5686 (m-80) REVERT: 2 38 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8175 (mp) REVERT: 2 63 SER cc_start: 0.8615 (p) cc_final: 0.8374 (p) REVERT: 2 73 TYR cc_start: 0.8619 (m-80) cc_final: 0.8131 (m-10) REVERT: 2 179 LEU cc_start: 0.9086 (mm) cc_final: 0.8843 (mt) REVERT: 2 188 ASP cc_start: 0.6651 (m-30) cc_final: 0.6209 (t70) REVERT: 6 90 ASN cc_start: 0.7054 (p0) cc_final: 0.6620 (p0) REVERT: g 30 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7214 (t80) REVERT: 9 25 CYS cc_start: 0.5440 (t) cc_final: 0.5203 (t) REVERT: C 523 ARG cc_start: 0.7262 (tpt-90) cc_final: 0.6915 (tpp-160) REVERT: A 73 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7262 (mmtt) REVERT: A 84 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8414 (mtm180) outliers start: 52 outliers final: 26 residues processed: 309 average time/residue: 0.3013 time to fit residues: 145.5897 Evaluate side-chains 274 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 116 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 254 SER Chi-restraints excluded: chain 2 residue 337 ILE Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 6 residue 36 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 88 LYS Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain 9 residue 64 LEU Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.1980 chunk 162 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN b 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20381 Z= 0.177 Angle : 0.549 9.057 27617 Z= 0.282 Chirality : 0.039 0.175 3178 Planarity : 0.004 0.060 3396 Dihedral : 11.049 158.517 2979 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.81 % Rotamer: Outliers : 2.39 % Allowed : 15.08 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2413 helix: 1.86 (0.13), residues: 1569 sheet: -1.14 (0.55), residues: 85 loop : -0.64 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 98 HIS 0.005 0.001 HIS C 583 PHE 0.026 0.001 PHE C 530 TYR 0.023 0.001 TYR A 194 ARG 0.003 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 261 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.7223 (m-30) cc_final: 0.6319 (m-30) REVERT: W 119 MET cc_start: 0.7187 (ptm) cc_final: 0.6952 (ptm) REVERT: X 19 TYR cc_start: 0.8294 (m-80) cc_final: 0.8044 (m-80) REVERT: X 109 LYS cc_start: 0.8183 (tppt) cc_final: 0.7535 (mttt) REVERT: X 115 MET cc_start: 0.6356 (mmt) cc_final: 0.6057 (mmt) REVERT: X 124 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7819 (mm-30) REVERT: 1 139 SER cc_start: 0.8274 (t) cc_final: 0.7673 (p) REVERT: 1 273 PHE cc_start: 0.6295 (t80) cc_final: 0.5803 (m-10) REVERT: 2 38 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8352 (mp) REVERT: 2 57 GLU cc_start: 0.8370 (mp0) cc_final: 0.8101 (mp0) REVERT: 2 73 TYR cc_start: 0.8542 (m-80) cc_final: 0.8133 (m-10) REVERT: 2 179 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8822 (mt) REVERT: 2 188 ASP cc_start: 0.6381 (m-30) cc_final: 0.5910 (t70) REVERT: 3 78 MET cc_start: 0.7654 (mmm) cc_final: 0.7352 (mmm) REVERT: 6 90 ASN cc_start: 0.6983 (p0) cc_final: 0.6549 (p0) REVERT: g 30 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.7226 (t80) REVERT: C 523 ARG cc_start: 0.7253 (tpt-90) cc_final: 0.6956 (tpp-160) REVERT: C 534 MET cc_start: 0.6763 (mpp) cc_final: 0.6091 (mpp) REVERT: C 804 TRP cc_start: 0.7445 (t60) cc_final: 0.7090 (t60) REVERT: C 842 MET cc_start: 0.8124 (mmm) cc_final: 0.7778 (mmm) REVERT: A 84 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8411 (mtm180) REVERT: A 159 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8268 (mptt) outliers start: 51 outliers final: 29 residues processed: 300 average time/residue: 0.3129 time to fit residues: 145.6794 Evaluate side-chains 275 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 82 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 254 SER Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 36 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 88 LYS Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain 9 residue 64 LEU Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 159 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN 1 173 GLN C 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20381 Z= 0.292 Angle : 0.605 9.340 27617 Z= 0.307 Chirality : 0.041 0.165 3178 Planarity : 0.004 0.056 3396 Dihedral : 10.638 153.903 2979 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.57 % Rotamer: Outliers : 3.00 % Allowed : 15.93 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2413 helix: 1.80 (0.13), residues: 1570 sheet: -0.96 (0.58), residues: 77 loop : -0.73 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 1 125 HIS 0.009 0.001 HIS C 583 PHE 0.017 0.002 PHE 9 41 TYR 0.024 0.002 TYR A 194 ARG 0.004 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 282 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 59 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: W 119 MET cc_start: 0.7067 (ptm) cc_final: 0.6665 (ptm) REVERT: X 23 ASP cc_start: 0.8509 (m-30) cc_final: 0.8278 (m-30) REVERT: X 109 LYS cc_start: 0.8014 (tppt) cc_final: 0.7368 (mttt) REVERT: 1 139 SER cc_start: 0.8310 (t) cc_final: 0.7735 (p) REVERT: 1 273 PHE cc_start: 0.6609 (t80) cc_final: 0.5826 (m-10) REVERT: 2 179 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8837 (mt) REVERT: 2 188 ASP cc_start: 0.6440 (m-30) cc_final: 0.6083 (t70) REVERT: 3 78 MET cc_start: 0.7713 (mmm) cc_final: 0.7488 (mmm) REVERT: 6 90 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.6912 (p0) REVERT: g 60 GLN cc_start: 0.8418 (mt0) cc_final: 0.7930 (tt0) REVERT: C 531 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.4986 (m-80) REVERT: C 534 MET cc_start: 0.7461 (mpp) cc_final: 0.6893 (mmt) REVERT: C 633 MET cc_start: 0.7611 (mtm) cc_final: 0.7378 (mtt) REVERT: C 723 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.5443 (mtt180) REVERT: C 804 TRP cc_start: 0.7425 (t60) cc_final: 0.6973 (t60) REVERT: C 842 MET cc_start: 0.8141 (mmm) cc_final: 0.7889 (mmm) REVERT: A 84 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8456 (mtm180) REVERT: A 159 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8380 (mptt) REVERT: A 209 LYS cc_start: 0.6060 (mmmt) cc_final: 0.5632 (mmtm) outliers start: 64 outliers final: 42 residues processed: 328 average time/residue: 0.3126 time to fit residues: 158.0471 Evaluate side-chains 299 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 250 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 1 residue 237 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 116 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 254 SER Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 36 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 88 LYS Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 41 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain 9 residue 64 LEU Chi-restraints excluded: chain C residue 531 TYR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 127 ASN U 169 ASN 1 173 GLN 2 29 ASN 2 50 GLN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20381 Z= 0.168 Angle : 0.538 8.106 27617 Z= 0.276 Chirality : 0.039 0.160 3178 Planarity : 0.004 0.057 3396 Dihedral : 10.324 156.897 2979 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 2.20 % Allowed : 17.42 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2413 helix: 2.05 (0.13), residues: 1570 sheet: -1.14 (0.58), residues: 73 loop : -0.71 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 98 HIS 0.005 0.001 HIS C 583 PHE 0.017 0.001 PHE D 5 TYR 0.024 0.001 TYR A 194 ARG 0.004 0.000 ARG U 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 277 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 59 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: W 94 GLU cc_start: 0.8296 (tp30) cc_final: 0.8062 (tp30) REVERT: W 119 MET cc_start: 0.7057 (ptm) cc_final: 0.6668 (ptm) REVERT: X 23 ASP cc_start: 0.8327 (m-30) cc_final: 0.8010 (m-30) REVERT: X 109 LYS cc_start: 0.7988 (tppt) cc_final: 0.7356 (mttt) REVERT: X 124 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7754 (mm-30) REVERT: 1 139 SER cc_start: 0.8317 (t) cc_final: 0.7800 (p) REVERT: 1 273 PHE cc_start: 0.6671 (t80) cc_final: 0.5915 (m-10) REVERT: 1 290 MET cc_start: 0.6314 (mpp) cc_final: 0.6106 (mpp) REVERT: 2 34 LEU cc_start: 0.8377 (tp) cc_final: 0.8049 (tp) REVERT: 2 38 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8317 (mp) REVERT: 2 57 GLU cc_start: 0.8489 (mp0) cc_final: 0.8114 (mp0) REVERT: 2 179 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (mt) REVERT: 2 188 ASP cc_start: 0.6363 (m-30) cc_final: 0.6055 (t70) REVERT: 6 90 ASN cc_start: 0.7148 (p0) cc_final: 0.6674 (p0) REVERT: g 60 GLN cc_start: 0.8412 (mt0) cc_final: 0.7925 (tt0) REVERT: 9 18 GLU cc_start: 0.7606 (mp0) cc_final: 0.7248 (mp0) REVERT: C 534 MET cc_start: 0.7408 (mpp) cc_final: 0.7137 (mmt) REVERT: C 633 MET cc_start: 0.7633 (mtm) cc_final: 0.7320 (mtm) REVERT: C 804 TRP cc_start: 0.7406 (t60) cc_final: 0.6890 (t60) REVERT: C 842 MET cc_start: 0.8080 (mmm) cc_final: 0.7792 (mmm) REVERT: A 70 LYS cc_start: 0.7562 (tppt) cc_final: 0.6929 (ptmt) REVERT: A 84 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8442 (mtm180) REVERT: A 159 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8329 (mptt) outliers start: 47 outliers final: 34 residues processed: 314 average time/residue: 0.3175 time to fit residues: 154.7698 Evaluate side-chains 302 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 263 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 168 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 193 optimal weight: 0.1980 chunk 128 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 43 ASN U 127 ASN 3 22 ASN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20381 Z= 0.171 Angle : 0.536 14.100 27617 Z= 0.272 Chirality : 0.038 0.163 3178 Planarity : 0.004 0.058 3396 Dihedral : 9.996 158.315 2979 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.31 % Favored : 95.57 % Rotamer: Outliers : 2.72 % Allowed : 17.14 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.18), residues: 2413 helix: 2.16 (0.13), residues: 1566 sheet: -1.16 (0.58), residues: 73 loop : -0.64 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 125 HIS 0.007 0.001 HIS C 583 PHE 0.014 0.001 PHE 3 94 TYR 0.025 0.001 TYR A 194 ARG 0.003 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 277 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 37 ASN cc_start: 0.8177 (t0) cc_final: 0.7947 (t0) REVERT: W 47 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7453 (mtp85) REVERT: W 78 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6235 (t0) REVERT: W 94 GLU cc_start: 0.8345 (tp30) cc_final: 0.8111 (tp30) REVERT: W 119 MET cc_start: 0.7033 (ptm) cc_final: 0.6665 (ptm) REVERT: X 23 ASP cc_start: 0.8279 (m-30) cc_final: 0.7943 (m-30) REVERT: X 76 ARG cc_start: 0.8073 (ttp-170) cc_final: 0.7822 (mtt90) REVERT: X 109 LYS cc_start: 0.7996 (tppt) cc_final: 0.7363 (mttt) REVERT: 1 139 SER cc_start: 0.8360 (t) cc_final: 0.7880 (p) REVERT: 1 273 PHE cc_start: 0.6672 (t80) cc_final: 0.5969 (m-10) REVERT: 2 34 LEU cc_start: 0.8355 (tp) cc_final: 0.8050 (tp) REVERT: 2 38 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8279 (mp) REVERT: 2 57 GLU cc_start: 0.8465 (mp0) cc_final: 0.8074 (mp0) REVERT: 2 179 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8793 (mt) REVERT: 2 188 ASP cc_start: 0.6378 (m-30) cc_final: 0.6099 (t70) REVERT: 6 30 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6496 (tmm) REVERT: 6 90 ASN cc_start: 0.7183 (p0) cc_final: 0.6751 (p0) REVERT: g 60 GLN cc_start: 0.8417 (mt0) cc_final: 0.7943 (tt0) REVERT: b 62 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6106 (tt0) REVERT: C 531 TYR cc_start: 0.6066 (t80) cc_final: 0.5083 (m-80) REVERT: C 633 MET cc_start: 0.7687 (mtm) cc_final: 0.7413 (mtm) REVERT: C 842 MET cc_start: 0.8050 (mmm) cc_final: 0.7777 (mmm) REVERT: A 70 LYS cc_start: 0.7499 (tppt) cc_final: 0.7050 (ptmt) REVERT: A 84 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8444 (mtm110) REVERT: A 159 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8335 (mptt) REVERT: A 209 LYS cc_start: 0.5916 (mmmt) cc_final: 0.5421 (mmtm) outliers start: 58 outliers final: 40 residues processed: 321 average time/residue: 0.3009 time to fit residues: 151.7914 Evaluate side-chains 309 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 263 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 1 residue 237 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 41 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 127 ASN 2 29 ASN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 20381 Z= 0.225 Angle : 0.573 13.278 27617 Z= 0.290 Chirality : 0.040 0.209 3178 Planarity : 0.004 0.072 3396 Dihedral : 9.852 158.655 2979 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.31 % Favored : 95.57 % Rotamer: Outliers : 2.90 % Allowed : 17.19 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2413 helix: 2.09 (0.13), residues: 1566 sheet: -1.12 (0.59), residues: 73 loop : -0.63 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 804 HIS 0.007 0.001 HIS C 583 PHE 0.027 0.001 PHE C 585 TYR 0.024 0.001 TYR A 194 ARG 0.004 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 275 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 33 TYR cc_start: 0.4416 (m-80) cc_final: 0.3972 (p90) REVERT: W 47 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7078 (mmm-85) REVERT: W 78 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6273 (t0) REVERT: W 94 GLU cc_start: 0.8213 (tp30) cc_final: 0.7995 (tp30) REVERT: W 119 MET cc_start: 0.7148 (ptm) cc_final: 0.6719 (ptm) REVERT: X 23 ASP cc_start: 0.8322 (m-30) cc_final: 0.8052 (m-30) REVERT: X 76 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7771 (mtt90) REVERT: X 109 LYS cc_start: 0.8022 (tppt) cc_final: 0.7371 (mttt) REVERT: 1 139 SER cc_start: 0.8292 (t) cc_final: 0.7813 (p) REVERT: 1 273 PHE cc_start: 0.6605 (t80) cc_final: 0.5861 (m-10) REVERT: 2 34 LEU cc_start: 0.8383 (tp) cc_final: 0.8092 (tp) REVERT: 2 38 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8336 (mp) REVERT: 2 57 GLU cc_start: 0.8494 (mp0) cc_final: 0.8077 (mp0) REVERT: 2 179 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8822 (mt) REVERT: 2 188 ASP cc_start: 0.6534 (m-30) cc_final: 0.5974 (t70) REVERT: 6 30 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6597 (tmm) REVERT: 6 90 ASN cc_start: 0.7248 (p0) cc_final: 0.6790 (p0) REVERT: g 60 GLN cc_start: 0.8373 (mt0) cc_final: 0.7894 (tt0) REVERT: b 62 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6144 (tt0) REVERT: 9 18 GLU cc_start: 0.7631 (mp0) cc_final: 0.7282 (mp0) REVERT: C 534 MET cc_start: 0.7575 (mmt) cc_final: 0.7321 (mmt) REVERT: C 633 MET cc_start: 0.7675 (mtm) cc_final: 0.7372 (mtm) REVERT: C 842 MET cc_start: 0.8078 (mmm) cc_final: 0.7843 (mmm) REVERT: A 70 LYS cc_start: 0.7526 (tppt) cc_final: 0.7115 (ptmt) REVERT: A 84 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8406 (mtm110) outliers start: 62 outliers final: 47 residues processed: 321 average time/residue: 0.3255 time to fit residues: 163.5180 Evaluate side-chains 322 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 270 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 98 THR Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 190 LEU Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain 9 residue 64 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 213 optimal weight: 30.0000 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 127 ASN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 20381 Z= 0.250 Angle : 0.581 13.254 27617 Z= 0.294 Chirality : 0.040 0.206 3178 Planarity : 0.004 0.061 3396 Dihedral : 9.748 159.626 2979 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.61 % Rotamer: Outliers : 2.62 % Allowed : 17.89 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2413 helix: 2.03 (0.13), residues: 1571 sheet: -1.21 (0.61), residues: 64 loop : -0.57 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 804 HIS 0.005 0.001 HIS C 583 PHE 0.025 0.001 PHE g 8 TYR 0.024 0.001 TYR A 194 ARG 0.004 0.000 ARG 9 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 289 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 33 TYR cc_start: 0.4408 (m-80) cc_final: 0.3921 (p90) REVERT: W 47 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7173 (mmm-85) REVERT: W 78 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.6117 (t0) REVERT: W 94 GLU cc_start: 0.8170 (tp30) cc_final: 0.7904 (tp30) REVERT: W 119 MET cc_start: 0.7168 (ptm) cc_final: 0.6734 (ptm) REVERT: X 76 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7804 (mtt90) REVERT: X 109 LYS cc_start: 0.8081 (tppt) cc_final: 0.7436 (mttt) REVERT: X 112 GLU cc_start: 0.7228 (tt0) cc_final: 0.6957 (mt-10) REVERT: 1 139 SER cc_start: 0.8323 (t) cc_final: 0.7847 (p) REVERT: 1 159 MET cc_start: 0.7580 (ttm) cc_final: 0.7240 (mtt) REVERT: 1 273 PHE cc_start: 0.6767 (t80) cc_final: 0.5909 (m-10) REVERT: 2 34 LEU cc_start: 0.8404 (tp) cc_final: 0.8125 (tp) REVERT: 2 38 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8365 (mp) REVERT: 2 179 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8834 (mt) REVERT: 2 188 ASP cc_start: 0.6299 (m-30) cc_final: 0.6008 (t70) REVERT: 6 30 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6607 (tmm) REVERT: 6 90 ASN cc_start: 0.7395 (p0) cc_final: 0.6889 (p0) REVERT: g 60 GLN cc_start: 0.8399 (mt0) cc_final: 0.8120 (mt0) REVERT: b 62 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6523 (tt0) REVERT: 9 34 ARG cc_start: 0.5235 (tpp-160) cc_final: 0.4607 (tpp-160) REVERT: C 633 MET cc_start: 0.7714 (mtm) cc_final: 0.7370 (mtm) REVERT: C 842 MET cc_start: 0.8141 (mmm) cc_final: 0.7888 (mmm) REVERT: A 70 LYS cc_start: 0.7562 (tppt) cc_final: 0.7204 (ptmt) REVERT: A 84 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8385 (mtm110) REVERT: A 113 ASP cc_start: 0.8309 (p0) cc_final: 0.8106 (p0) outliers start: 56 outliers final: 47 residues processed: 328 average time/residue: 0.3187 time to fit residues: 163.6643 Evaluate side-chains 324 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 272 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 98 THR Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 190 LEU Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 237 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 0.0970 chunk 149 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20381 Z= 0.207 Angle : 0.564 13.081 27617 Z= 0.286 Chirality : 0.039 0.219 3178 Planarity : 0.004 0.059 3396 Dihedral : 9.522 160.165 2979 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.48 % Favored : 95.40 % Rotamer: Outliers : 2.39 % Allowed : 18.78 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.17), residues: 2413 helix: 2.12 (0.13), residues: 1564 sheet: -1.25 (0.64), residues: 62 loop : -0.57 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 804 HIS 0.003 0.001 HIS C 583 PHE 0.026 0.001 PHE g 8 TYR 0.025 0.001 TYR A 194 ARG 0.003 0.000 ARG D 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 279 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 33 TYR cc_start: 0.4423 (m-80) cc_final: 0.3911 (p90) REVERT: W 47 ARG cc_start: 0.7685 (mmm160) cc_final: 0.7160 (mmm-85) REVERT: W 78 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.6107 (t0) REVERT: W 94 GLU cc_start: 0.8118 (tp30) cc_final: 0.7873 (tp30) REVERT: W 119 MET cc_start: 0.7102 (ptm) cc_final: 0.6725 (ptm) REVERT: X 109 LYS cc_start: 0.8076 (tppt) cc_final: 0.7440 (mttt) REVERT: 1 139 SER cc_start: 0.8286 (t) cc_final: 0.7831 (p) REVERT: 1 159 MET cc_start: 0.7509 (ttm) cc_final: 0.7203 (mtt) REVERT: 1 273 PHE cc_start: 0.6746 (t80) cc_final: 0.5879 (m-10) REVERT: 2 34 LEU cc_start: 0.8316 (tp) cc_final: 0.8107 (tp) REVERT: 2 38 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8385 (mp) REVERT: 2 57 GLU cc_start: 0.8481 (mp0) cc_final: 0.7994 (mp0) REVERT: 2 179 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8799 (mt) REVERT: 2 188 ASP cc_start: 0.6322 (m-30) cc_final: 0.6005 (t70) REVERT: 6 30 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6572 (tmm) REVERT: 6 90 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6790 (p0) REVERT: g 60 GLN cc_start: 0.8404 (mt0) cc_final: 0.8101 (mt0) REVERT: b 62 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6621 (tt0) REVERT: 9 18 GLU cc_start: 0.7588 (mp0) cc_final: 0.7369 (mp0) REVERT: 9 34 ARG cc_start: 0.5208 (tpp-160) cc_final: 0.4976 (tpp-160) REVERT: C 531 TYR cc_start: 0.5993 (t80) cc_final: 0.5171 (m-80) REVERT: C 633 MET cc_start: 0.7688 (mtm) cc_final: 0.7344 (mtm) REVERT: C 842 MET cc_start: 0.8116 (mmm) cc_final: 0.7869 (mmm) REVERT: A 70 LYS cc_start: 0.7579 (tppt) cc_final: 0.7206 (ptmt) REVERT: A 84 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8358 (mtm110) outliers start: 51 outliers final: 44 residues processed: 313 average time/residue: 0.3144 time to fit residues: 154.2227 Evaluate side-chains 316 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 83 TYR Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 190 LEU Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain 9 residue 64 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN 9 40 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100144 restraints weight = 29207.353| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.21 r_work: 0.3179 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20381 Z= 0.238 Angle : 0.579 12.946 27617 Z= 0.293 Chirality : 0.040 0.211 3178 Planarity : 0.004 0.059 3396 Dihedral : 9.451 160.336 2979 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.44 % Rotamer: Outliers : 2.62 % Allowed : 18.59 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2413 helix: 2.06 (0.13), residues: 1575 sheet: -1.21 (0.60), residues: 74 loop : -0.53 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 795 HIS 0.007 0.001 HIS C 800 PHE 0.034 0.001 PHE 1 228 TYR 0.025 0.001 TYR A 194 ARG 0.006 0.000 ARG X 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.53 seconds wall clock time: 79 minutes 41.31 seconds (4781.31 seconds total)