Starting phenix.real_space_refine on Wed Feb 21 02:15:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg4_33185/02_2024/7xg4_33185_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4742 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 134 5.49 5 S 105 5.16 5 C 15199 2.51 5 N 4385 2.21 5 O 4945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 328": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F GLU 320": "OE1" <-> "OE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H GLU 179": "OE1" <-> "OE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 406": "OE1" <-> "OE2" Residue "L GLU 437": "OE1" <-> "OE2" Residue "L GLU 443": "OE1" <-> "OE2" Residue "L GLU 474": "OE1" <-> "OE2" Residue "L GLU 576": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24769 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1897 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1709 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2488 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2503 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2450 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 1 Chain: "F" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2450 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 1 Chain: "G" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2131 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 17, 'TRANS': 262} Chain breaks: 1 Chain: "H" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "I" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1317 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 17} Link IDs: {'rna2p': 19, 'rna3p': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 722 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "K" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 759 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "L" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4542 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 31, 'TRANS': 562} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 226 SG CYS A 30 43.214 103.239 20.220 1.00 77.19 S ATOM 248 SG CYS A 33 39.702 102.688 19.640 1.00 77.19 S ATOM 526 SG CYS A 69 40.103 103.559 20.560 1.00 77.28 S Time building chain proxies: 14.58, per 1000 atoms: 0.59 Number of scatterers: 24769 At special positions: 0 Unit cell: (127.6, 143, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 105 16.00 P 134 15.00 O 4945 8.00 N 4385 7.00 C 15199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.39 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 30 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 31 sheets defined 33.4% alpha, 13.6% beta 21 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 10.87 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.641A pdb=" N ASP A 9 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.588A pdb=" N TYR A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'C' and resid 67 through 81 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 200 through 222 Processing helix chain 'C' and resid 269 through 284 removed outlier: 5.163A pdb=" N THR C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 184 through 187 Processing helix chain 'D' and resid 201 through 222 Processing helix chain 'D' and resid 269 through 282 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'E' and resid 67 through 81 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 96 through 104 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.969A pdb=" N VAL F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 282 through 284 No H-bonds generated for 'chain 'F' and resid 282 through 284' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'G' and resid 67 through 81 Processing helix chain 'G' and resid 83 through 88 Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 118 through 124 Processing helix chain 'G' and resid 269 through 283 removed outlier: 4.597A pdb=" N THR G 283 " --> pdb=" O LEU G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 331 Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 32 through 39 Processing helix chain 'H' and resid 70 through 94 Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 132 through 139 Processing helix chain 'H' and resid 141 through 163 removed outlier: 3.871A pdb=" N VAL H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'L' and resid 11 through 13 No H-bonds generated for 'chain 'L' and resid 11 through 13' Processing helix chain 'L' and resid 16 through 30 Proline residue: L 20 - end of helix removed outlier: 3.555A pdb=" N GLN L 24 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR L 29 " --> pdb=" O ALA L 26 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA L 30 " --> pdb=" O GLU L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' Processing helix chain 'L' and resid 45 through 59 removed outlier: 3.913A pdb=" N LYS L 59 " --> pdb=" O ALA L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 78 removed outlier: 4.144A pdb=" N TRP L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN L 74 " --> pdb=" O ALA L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 88 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 102 through 112 Processing helix chain 'L' and resid 115 through 121 Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 147 through 153 removed outlier: 3.539A pdb=" N LEU L 153 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 162 No H-bonds generated for 'chain 'L' and resid 159 through 162' Processing helix chain 'L' and resid 173 through 186 removed outlier: 4.350A pdb=" N SER L 183 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN L 184 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYR L 185 " --> pdb=" O MET L 181 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR L 186 " --> pdb=" O ARG L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 238 through 248 removed outlier: 4.734A pdb=" N GLU L 242 " --> pdb=" O HIS L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 263 removed outlier: 3.597A pdb=" N GLU L 263 " --> pdb=" O MET L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 286 removed outlier: 3.942A pdb=" N VAL L 286 " --> pdb=" O THR L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 318 Processing helix chain 'L' and resid 329 through 344 Processing helix chain 'L' and resid 371 through 379 Processing helix chain 'L' and resid 399 through 404 Processing helix chain 'L' and resid 421 through 425 removed outlier: 4.110A pdb=" N ALA L 425 " --> pdb=" O TRP L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 442 through 458 Processing helix chain 'L' and resid 470 through 487 removed outlier: 5.490A pdb=" N ALA L 482 " --> pdb=" O GLY L 478 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA L 483 " --> pdb=" O ARG L 479 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP L 486 " --> pdb=" O ALA L 482 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ARG L 487 " --> pdb=" O ALA L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 510 Processing helix chain 'L' and resid 520 through 522 No H-bonds generated for 'chain 'L' and resid 520 through 522' Processing helix chain 'L' and resid 537 through 539 No H-bonds generated for 'chain 'L' and resid 537 through 539' Processing helix chain 'L' and resid 559 through 568 Processing helix chain 'L' and resid 570 through 587 removed outlier: 4.034A pdb=" N ARG L 587 " --> pdb=" O GLN L 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 615 through 622 removed outlier: 3.745A pdb=" N ILE L 619 " --> pdb=" O PRO L 615 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU L 620 " --> pdb=" O PHE L 616 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.672A pdb=" N ALA A 84 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 115 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 114 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 72 through 75 removed outlier: 5.960A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 80 through 86 Processing sheet with id= E, first strand: chain 'B' and resid 196 through 200 Processing sheet with id= F, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.180A pdb=" N ARG C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 300 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 21 through 23 Processing sheet with id= H, first strand: chain 'C' and resid 45 through 50 Processing sheet with id= I, first strand: chain 'C' and resid 174 through 181 Processing sheet with id= J, first strand: chain 'D' and resid 144 through 146 removed outlier: 5.999A pdb=" N ARG D 8 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE D 300 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.982A pdb=" N ASN D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 45 through 50 Processing sheet with id= M, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= N, first strand: chain 'E' and resid 302 through 305 Processing sheet with id= O, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.684A pdb=" N ASN E 21 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 45 through 51 Processing sheet with id= Q, first strand: chain 'E' and resid 174 through 181 Processing sheet with id= R, first strand: chain 'F' and resid 144 through 146 removed outlier: 6.112A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE F 300 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 21 through 23 Processing sheet with id= T, first strand: chain 'F' and resid 174 through 180 Processing sheet with id= U, first strand: chain 'F' and resid 45 through 53 removed outlier: 7.008A pdb=" N VAL F 56 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 298 through 300 removed outlier: 3.505A pdb=" N LEU G 256 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.747A pdb=" N ASN G 21 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA G 248 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= Y, first strand: chain 'H' and resid 102 through 109 Processing sheet with id= Z, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.939A pdb=" N GLY H 177 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU H 203 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE H 175 " --> pdb=" O GLU H 203 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 180 through 185 Processing sheet with id= AB, first strand: chain 'H' and resid 211 through 213 removed outlier: 4.042A pdb=" N TRP H 212 " --> pdb=" O ILE H 225 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE H 225 " --> pdb=" O TRP H 212 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'L' and resid 412 through 414 removed outlier: 6.058A pdb=" N ILE L 34 " --> pdb=" O ALA L 413 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA L 384 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA L 37 " --> pdb=" O ALA L 384 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU L 386 " --> pdb=" O ALA L 37 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 251 through 254 Processing sheet with id= AE, first strand: chain 'L' and resid 427 through 429 removed outlier: 6.402A pdb=" N LYS L 597 " --> pdb=" O LEU L 428 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 8.45 Time building geometry restraints manager: 12.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 3811 1.27 - 1.41: 6493 1.41 - 1.55: 14680 1.55 - 1.68: 385 1.68 - 1.82: 187 Bond restraints: 25556 Sorted by residual: bond pdb=" O3' 23G I 61 " pdb=" PC 23G I 61 " ideal model delta sigma weight residual 1.334 1.603 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C4' 23G I 61 " pdb=" O4' 23G I 61 " ideal model delta sigma weight residual 1.663 1.429 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C4' 23G I 61 " pdb=" C3' 23G I 61 " ideal model delta sigma weight residual 1.302 1.516 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C2' 23G I 61 " pdb=" O2' 23G I 61 " ideal model delta sigma weight residual 1.250 1.427 -0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" CG1 ILE B 151 " pdb=" CD1 ILE B 151 " ideal model delta sigma weight residual 1.513 1.181 0.332 3.90e-02 6.57e+02 7.27e+01 ... (remaining 25551 not shown) Histogram of bond angle deviations from ideal: 92.63 - 101.32: 84 101.32 - 110.01: 6121 110.01 - 118.70: 15365 118.70 - 127.39: 13230 127.39 - 136.09: 483 Bond angle restraints: 35283 Sorted by residual: angle pdb=" C3' A I 38 " pdb=" C2' A I 38 " pdb=" O2' A I 38 " ideal model delta sigma weight residual 114.60 126.04 -11.44 1.50e+00 4.44e-01 5.81e+01 angle pdb=" O3' A I 38 " pdb=" C3' A I 38 " pdb=" C2' A I 38 " ideal model delta sigma weight residual 109.50 119.44 -9.94 1.50e+00 4.44e-01 4.39e+01 angle pdb=" C VAL E 65 " pdb=" CA VAL E 65 " pdb=" CB VAL E 65 " ideal model delta sigma weight residual 110.13 115.75 -5.62 9.70e-01 1.06e+00 3.36e+01 angle pdb=" N ILE C 185 " pdb=" CA ILE C 185 " pdb=" C ILE C 185 " ideal model delta sigma weight residual 112.80 106.15 6.65 1.15e+00 7.56e-01 3.34e+01 angle pdb=" C4' U I 21 " pdb=" C3' U I 21 " pdb=" O3' U I 21 " ideal model delta sigma weight residual 109.40 100.75 8.65 1.50e+00 4.44e-01 3.33e+01 ... (remaining 35278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 14286 35.11 - 70.22: 850 70.22 - 105.34: 50 105.34 - 140.45: 8 140.45 - 175.56: 4 Dihedral angle restraints: 15198 sinusoidal: 7060 harmonic: 8138 Sorted by residual: dihedral pdb=" O4' C I 6 " pdb=" C1' C I 6 " pdb=" N1 C I 6 " pdb=" C2 C I 6 " ideal model delta sinusoidal sigma weight residual 200.00 60.16 139.84 1 1.50e+01 4.44e-03 7.53e+01 dihedral pdb=" O4' U I 33 " pdb=" C1' U I 33 " pdb=" N1 U I 33 " pdb=" C2 U I 33 " ideal model delta sinusoidal sigma weight residual -160.00 -45.17 -114.83 1 1.50e+01 4.44e-03 6.06e+01 dihedral pdb=" O4' C I 20 " pdb=" C1' C I 20 " pdb=" N1 C I 20 " pdb=" C2 C I 20 " ideal model delta sinusoidal sigma weight residual -160.00 -46.40 -113.60 1 1.50e+01 4.44e-03 5.98e+01 ... (remaining 15195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3647 0.121 - 0.242: 349 0.242 - 0.363: 17 0.363 - 0.484: 5 0.484 - 0.605: 3 Chirality restraints: 4021 Sorted by residual: chirality pdb=" CG LEU H 167 " pdb=" CB LEU H 167 " pdb=" CD1 LEU H 167 " pdb=" CD2 LEU H 167 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C2' A I 38 " pdb=" C3' A I 38 " pdb=" O2' A I 38 " pdb=" C1' A I 38 " both_signs ideal model delta sigma weight residual False -2.52 -1.95 -0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CG LEU B 130 " pdb=" CB LEU B 130 " pdb=" CD1 LEU B 130 " pdb=" CD2 LEU B 130 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 4018 not shown) Planarity restraints: 4095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 392 " -0.014 2.00e-02 2.50e+03 5.99e-02 6.27e+01 pdb=" CG PHE L 392 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 PHE L 392 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 PHE L 392 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE L 392 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 PHE L 392 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE L 392 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 153 " 0.017 2.00e-02 2.50e+03 5.44e-02 4.44e+01 pdb=" CG HIS G 153 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS G 153 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 HIS G 153 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS G 153 " 0.092 2.00e-02 2.50e+03 pdb=" NE2 HIS G 153 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 260 " 0.057 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP E 260 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP E 260 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 260 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 260 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP E 260 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP E 260 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 260 " 0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 260 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP E 260 " -0.004 2.00e-02 2.50e+03 ... (remaining 4092 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 33 1.93 - 2.67: 1111 2.67 - 3.41: 35332 3.41 - 4.16: 67067 4.16 - 4.90: 112913 Nonbonded interactions: 216456 Sorted by model distance: nonbonded pdb=" N SER C 117 " pdb=" OE2 GLU C 120 " model vdw 1.187 2.520 nonbonded pdb=" CD1 LEU B 21 " pdb=" OP1 G I 3 " model vdw 1.533 3.460 nonbonded pdb=" N1 A I 16 " pdb=" O4 DT K 36 " model vdw 1.542 2.496 nonbonded pdb=" OD1 ASN E 9 " pdb=" CD2 LEU E 256 " model vdw 1.570 3.460 nonbonded pdb=" C ASN F 166 " pdb=" OE1 GLU F 167 " model vdw 1.608 3.270 ... (remaining 216451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'D' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'E' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'F' and (resid 1 through 217 or resid 240 through 344)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 10.660 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 79.870 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 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 : 0.011 0.332 25556 Z= 0.681 Angle : 1.238 11.831 35283 Z= 0.732 Chirality : 0.073 0.605 4021 Planarity : 0.010 0.117 4095 Dihedral : 20.308 175.561 9982 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 37.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 1.33 % Allowed : 22.41 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.14), residues: 2842 helix: -1.27 (0.15), residues: 1046 sheet: -0.49 (0.24), residues: 447 loop : -1.29 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP H 212 HIS 0.083 0.003 HIS G 153 PHE 0.113 0.004 PHE L 392 TYR 0.055 0.005 TYR G 103 ARG 0.046 0.001 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 374 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: B 166 LYS cc_start: 0.7713 (tmmt) cc_final: 0.7459 (pptt) REVERT: B 182 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5212 (pp) REVERT: C 295 TYR cc_start: 0.7861 (m-10) cc_final: 0.7619 (m-10) REVERT: E 70 MET cc_start: 0.8078 (mmm) cc_final: 0.7602 (mmm) REVERT: F 168 MET cc_start: 0.4629 (tpp) cc_final: 0.3704 (mmm) REVERT: F 282 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5614 (mmm) REVERT: L 197 MET cc_start: 0.3171 (tpt) cc_final: 0.2466 (tpp) REVERT: L 205 MET cc_start: 0.5339 (mmp) cc_final: 0.4857 (mmm) REVERT: L 226 LEU cc_start: 0.2038 (mp) cc_final: 0.1568 (mt) REVERT: L 552 PRO cc_start: 0.5476 (Cg_endo) cc_final: 0.5216 (Cg_exo) REVERT: L 562 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6196 (mt-10) outliers start: 31 outliers final: 16 residues processed: 393 average time/residue: 0.3657 time to fit residues: 226.7658 Evaluate side-chains 346 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 327 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 103 GLN B 150 GLN C 2 GLN C 81 HIS ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN E 205 ASN F 21 ASN F 30 ASN F 343 GLN H 129 GLN ** H 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 25556 Z= 0.340 Angle : 0.797 11.813 35283 Z= 0.408 Chirality : 0.048 0.269 4021 Planarity : 0.006 0.086 4095 Dihedral : 20.800 179.773 4882 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.98 % Allowed : 19.92 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.15), residues: 2842 helix: -0.68 (0.15), residues: 1038 sheet: -0.53 (0.24), residues: 445 loop : -1.02 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 258 HIS 0.008 0.002 HIS D 153 PHE 0.024 0.002 PHE A 104 TYR 0.024 0.003 TYR A 141 ARG 0.013 0.001 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 368 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7492 (p90) cc_final: 0.7097 (p90) REVERT: C 140 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7148 (tt) REVERT: C 157 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5010 (tp30) REVERT: C 293 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8027 (mppt) REVERT: D 182 MET cc_start: 0.6651 (ptm) cc_final: 0.6264 (ptp) REVERT: E 6 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.6981 (p) REVERT: E 73 LEU cc_start: 0.9175 (tp) cc_final: 0.8968 (tt) REVERT: E 167 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6001 (tp30) REVERT: E 209 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7828 (pm20) REVERT: F 57 ILE cc_start: 0.7703 (mm) cc_final: 0.7398 (pt) REVERT: F 70 MET cc_start: 0.6149 (mtp) cc_final: 0.5921 (mtp) REVERT: F 149 LEU cc_start: 0.6588 (tp) cc_final: 0.6360 (tp) REVERT: F 194 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7220 (p) REVERT: F 210 ASP cc_start: 0.7558 (m-30) cc_final: 0.7289 (m-30) REVERT: G 44 ARG cc_start: 0.7351 (tpp80) cc_final: 0.6735 (mmt180) REVERT: G 51 ASP cc_start: 0.7667 (t0) cc_final: 0.7358 (t0) REVERT: G 64 ILE cc_start: 0.8085 (pt) cc_final: 0.7655 (mm) REVERT: G 103 TYR cc_start: 0.6200 (m-80) cc_final: 0.5593 (m-80) REVERT: G 129 PHE cc_start: 0.7752 (t80) cc_final: 0.7521 (t80) REVERT: G 160 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4399 (pp) REVERT: G 168 MET cc_start: 0.6508 (mmp) cc_final: 0.5570 (mmm) REVERT: H 167 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.5663 (tp) REVERT: L 129 SER cc_start: 0.6109 (OUTLIER) cc_final: 0.5624 (m) REVERT: L 197 MET cc_start: 0.3436 (tpt) cc_final: 0.3085 (tpp) REVERT: L 415 LEU cc_start: 0.6737 (mm) cc_final: 0.6386 (mt) REVERT: L 504 PHE cc_start: 0.5314 (t80) cc_final: 0.5110 (t80) REVERT: L 559 LEU cc_start: 0.5571 (OUTLIER) cc_final: 0.5065 (mt) REVERT: L 562 GLU cc_start: 0.7049 (mm-30) cc_final: 0.5821 (mt-10) outliers start: 116 outliers final: 63 residues processed: 447 average time/residue: 0.3550 time to fit residues: 253.7121 Evaluate side-chains 383 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 310 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 405 LEU Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 613 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.0040 chunk 223 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 0.0980 chunk 290 optimal weight: 1.9990 chunk 239 optimal weight: 0.0870 chunk 267 optimal weight: 40.0000 chunk 91 optimal weight: 0.0970 chunk 216 optimal weight: 6.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25556 Z= 0.201 Angle : 0.668 12.873 35283 Z= 0.343 Chirality : 0.043 0.228 4021 Planarity : 0.005 0.062 4095 Dihedral : 20.556 177.812 4848 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.42 % Allowed : 22.24 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.15), residues: 2842 helix: -0.25 (0.16), residues: 1033 sheet: -0.48 (0.24), residues: 444 loop : -0.94 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 600 HIS 0.005 0.001 HIS D 291 PHE 0.022 0.002 PHE A 104 TYR 0.015 0.002 TYR A 79 ARG 0.012 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 364 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.6744 (mt0) cc_final: 0.6513 (tm-30) REVERT: A 200 GLU cc_start: 0.8256 (tp30) cc_final: 0.7957 (mm-30) REVERT: A 204 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5616 (t80) REVERT: C 140 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7166 (tt) REVERT: C 157 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5019 (tp30) REVERT: D 59 SER cc_start: 0.6291 (OUTLIER) cc_final: 0.6035 (p) REVERT: D 182 MET cc_start: 0.6444 (ptm) cc_final: 0.6196 (ptp) REVERT: F 57 ILE cc_start: 0.7830 (mm) cc_final: 0.7391 (pt) REVERT: F 149 LEU cc_start: 0.6256 (tp) cc_final: 0.5904 (tp) REVERT: F 175 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6263 (tm-30) REVERT: G 51 ASP cc_start: 0.7660 (t0) cc_final: 0.7413 (t0) REVERT: G 120 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7656 (mt-10) REVERT: G 160 LEU cc_start: 0.4746 (OUTLIER) cc_final: 0.4336 (pp) REVERT: G 282 MET cc_start: 0.6559 (tpp) cc_final: 0.6246 (tpp) REVERT: H 22 LEU cc_start: 0.7462 (tt) cc_final: 0.7237 (tt) REVERT: H 167 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.5572 (tp) REVERT: H 224 HIS cc_start: 0.6077 (OUTLIER) cc_final: 0.5630 (p90) REVERT: L 197 MET cc_start: 0.3284 (tpt) cc_final: 0.2450 (tpp) REVERT: L 226 LEU cc_start: 0.2305 (mp) cc_final: 0.2070 (mt) REVERT: L 396 ASP cc_start: 0.7171 (p0) cc_final: 0.6416 (m-30) REVERT: L 415 LEU cc_start: 0.6879 (mm) cc_final: 0.6548 (mt) REVERT: L 504 PHE cc_start: 0.5386 (t80) cc_final: 0.5182 (t80) REVERT: L 552 PRO cc_start: 0.5784 (Cg_endo) cc_final: 0.5490 (Cg_exo) REVERT: L 559 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5055 (mt) REVERT: L 562 GLU cc_start: 0.7095 (mm-30) cc_final: 0.5978 (mt-10) outliers start: 103 outliers final: 46 residues processed: 437 average time/residue: 0.3396 time to fit residues: 237.9815 Evaluate side-chains 381 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 326 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 224 HIS Chi-restraints excluded: chain L residue 405 LEU Chi-restraints excluded: chain L residue 443 GLU Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 40.0000 chunk 202 optimal weight: 0.8980 chunk 139 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN C 249 HIS ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 GLN L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 583 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25556 Z= 0.207 Angle : 0.652 18.640 35283 Z= 0.334 Chirality : 0.043 0.224 4021 Planarity : 0.005 0.062 4095 Dihedral : 20.455 178.208 4842 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.94 % Allowed : 22.16 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.15), residues: 2842 helix: 0.03 (0.16), residues: 1041 sheet: -0.54 (0.24), residues: 448 loop : -0.83 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 600 HIS 0.007 0.001 HIS H 85 PHE 0.020 0.002 PHE A 104 TYR 0.019 0.002 TYR G 103 ARG 0.010 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 356 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8231 (tp30) cc_final: 0.7902 (mm-30) REVERT: A 204 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5593 (t80) REVERT: A 219 MET cc_start: 0.4391 (mtp) cc_final: 0.4163 (mtp) REVERT: C 140 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7131 (tt) REVERT: C 157 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.4956 (tp30) REVERT: C 250 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: C 294 ASP cc_start: 0.6726 (t0) cc_final: 0.6261 (t0) REVERT: C 337 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5700 (mp0) REVERT: D 59 SER cc_start: 0.6473 (OUTLIER) cc_final: 0.6216 (p) REVERT: F 57 ILE cc_start: 0.7817 (mm) cc_final: 0.7520 (mt) REVERT: F 149 LEU cc_start: 0.6540 (tp) cc_final: 0.6146 (tp) REVERT: F 175 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6338 (tm-30) REVERT: F 194 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.7112 (p) REVERT: G 40 LEU cc_start: 0.5025 (OUTLIER) cc_final: 0.4731 (tp) REVERT: G 51 ASP cc_start: 0.7663 (t0) cc_final: 0.7374 (t0) REVERT: G 120 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7688 (mt-10) REVERT: G 160 LEU cc_start: 0.4604 (OUTLIER) cc_final: 0.4207 (pp) REVERT: G 264 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5823 (tp) REVERT: H 167 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.5784 (tp) REVERT: H 224 HIS cc_start: 0.6000 (OUTLIER) cc_final: 0.5525 (p90) REVERT: L 129 SER cc_start: 0.5743 (OUTLIER) cc_final: 0.5105 (m) REVERT: L 192 LEU cc_start: 0.1755 (OUTLIER) cc_final: 0.1550 (mp) REVERT: L 197 MET cc_start: 0.3212 (tpt) cc_final: 0.2258 (tpp) REVERT: L 226 LEU cc_start: 0.2887 (mp) cc_final: 0.2530 (mt) REVERT: L 415 LEU cc_start: 0.6973 (mm) cc_final: 0.6613 (mt) REVERT: L 552 PRO cc_start: 0.5864 (Cg_endo) cc_final: 0.5528 (Cg_exo) REVERT: L 562 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6004 (mt-10) outliers start: 115 outliers final: 68 residues processed: 432 average time/residue: 0.3345 time to fit residues: 233.6690 Evaluate side-chains 397 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 314 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 224 HIS Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 443 GLU Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 244 optimal weight: 0.0980 chunk 197 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 284 ASN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25556 Z= 0.312 Angle : 0.723 14.893 35283 Z= 0.370 Chirality : 0.045 0.242 4021 Planarity : 0.005 0.056 4095 Dihedral : 20.543 179.087 4839 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.71 % Allowed : 22.93 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.15), residues: 2842 helix: 0.12 (0.16), residues: 1012 sheet: -0.65 (0.24), residues: 449 loop : -0.90 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 600 HIS 0.007 0.001 HIS C 249 PHE 0.026 0.002 PHE L 36 TYR 0.017 0.002 TYR G 103 ARG 0.010 0.001 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 326 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8257 (tp30) cc_final: 0.7931 (mm-30) REVERT: A 204 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.5607 (t80) REVERT: A 219 MET cc_start: 0.4792 (mtp) cc_final: 0.3963 (mtp) REVERT: C 140 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7122 (tt) REVERT: C 250 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: C 294 ASP cc_start: 0.6708 (t0) cc_final: 0.6111 (t0) REVERT: D 59 SER cc_start: 0.6650 (OUTLIER) cc_final: 0.6360 (p) REVERT: F 175 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: F 194 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7303 (p) REVERT: G 40 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.5001 (tp) REVERT: G 45 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6983 (tpt) REVERT: G 51 ASP cc_start: 0.7656 (t0) cc_final: 0.7441 (t0) REVERT: G 120 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7616 (mt-10) REVERT: G 160 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4400 (pp) REVERT: G 264 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6177 (tp) REVERT: L 129 SER cc_start: 0.5323 (OUTLIER) cc_final: 0.4893 (m) REVERT: L 197 MET cc_start: 0.3191 (tpt) cc_final: 0.2214 (tpp) REVERT: L 504 PHE cc_start: 0.5733 (t80) cc_final: 0.5376 (t80) outliers start: 133 outliers final: 91 residues processed: 418 average time/residue: 0.3326 time to fit residues: 225.8093 Evaluate side-chains 407 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 305 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 352 ILE Chi-restraints excluded: chain L residue 443 GLU Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 613 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.0070 chunk 257 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 237 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS H 56 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 HIS L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25556 Z= 0.211 Angle : 0.661 12.084 35283 Z= 0.335 Chirality : 0.043 0.290 4021 Planarity : 0.005 0.054 4095 Dihedral : 20.475 179.006 4839 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.55 % Allowed : 25.03 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.16), residues: 2842 helix: 0.34 (0.17), residues: 1010 sheet: -0.62 (0.24), residues: 440 loop : -0.81 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 258 HIS 0.022 0.001 HIS H 224 PHE 0.019 0.002 PHE A 104 TYR 0.017 0.002 TYR C 295 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 347 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7668 (mmp80) cc_final: 0.7379 (mmp80) REVERT: A 200 GLU cc_start: 0.8168 (tp30) cc_final: 0.7847 (mm-30) REVERT: A 204 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5572 (t80) REVERT: C 140 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7097 (tt) REVERT: C 294 ASP cc_start: 0.6459 (t0) cc_final: 0.5967 (t0) REVERT: C 295 TYR cc_start: 0.7746 (m-10) cc_final: 0.7442 (m-80) REVERT: D 323 PHE cc_start: 0.7605 (m-10) cc_final: 0.7204 (m-10) REVERT: F 30 ASN cc_start: 0.8031 (m-40) cc_final: 0.7815 (t0) REVERT: F 175 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: F 194 VAL cc_start: 0.7421 (OUTLIER) cc_final: 0.7173 (p) REVERT: G 51 ASP cc_start: 0.7622 (t0) cc_final: 0.7405 (t0) REVERT: G 120 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7621 (mt-10) REVERT: G 160 LEU cc_start: 0.4808 (OUTLIER) cc_final: 0.4372 (pp) REVERT: G 264 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6160 (tp) REVERT: G 282 MET cc_start: 0.6342 (tpp) cc_final: 0.6049 (tpp) REVERT: L 129 SER cc_start: 0.5199 (OUTLIER) cc_final: 0.4741 (m) REVERT: L 197 MET cc_start: 0.2987 (tpt) cc_final: 0.2012 (tpp) REVERT: L 504 PHE cc_start: 0.5625 (t80) cc_final: 0.5347 (t80) outliers start: 106 outliers final: 72 residues processed: 421 average time/residue: 0.3318 time to fit residues: 227.2721 Evaluate side-chains 395 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 316 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 352 ILE Chi-restraints excluded: chain L residue 443 GLU Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 173 optimal weight: 0.0270 chunk 131 optimal weight: 1.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 HIS L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 583 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25556 Z= 0.278 Angle : 0.701 12.525 35283 Z= 0.356 Chirality : 0.044 0.247 4021 Planarity : 0.005 0.055 4095 Dihedral : 20.425 178.896 4839 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.37 % Allowed : 24.65 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.16), residues: 2842 helix: 0.30 (0.17), residues: 1008 sheet: -0.65 (0.24), residues: 439 loop : -0.85 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 600 HIS 0.018 0.001 HIS H 224 PHE 0.020 0.002 PHE D 246 TYR 0.018 0.002 TYR G 99 ARG 0.010 0.001 ARG L 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 337 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8228 (tp30) cc_final: 0.7787 (mm-30) REVERT: A 204 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5520 (t80) REVERT: C 140 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7075 (tt) REVERT: C 250 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: C 266 ARG cc_start: 0.7416 (mtm110) cc_final: 0.7174 (mtm-85) REVERT: C 294 ASP cc_start: 0.6744 (t0) cc_final: 0.6544 (t0) REVERT: E 164 TYR cc_start: 0.6029 (m-80) cc_final: 0.5779 (m-80) REVERT: F 30 ASN cc_start: 0.8228 (m-40) cc_final: 0.7951 (t0) REVERT: F 175 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: F 194 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7284 (p) REVERT: G 40 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5207 (tp) REVERT: G 51 ASP cc_start: 0.7537 (t0) cc_final: 0.7329 (t0) REVERT: G 120 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7557 (mt-10) REVERT: G 160 LEU cc_start: 0.4695 (OUTLIER) cc_final: 0.4290 (pp) REVERT: G 264 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6275 (tp) REVERT: H 39 MET cc_start: 0.5676 (mmm) cc_final: 0.4903 (mmt) REVERT: H 62 GLN cc_start: 0.7743 (mp10) cc_final: 0.7486 (mp10) REVERT: L 47 ARG cc_start: 0.5686 (mmt90) cc_final: 0.5264 (mmt90) REVERT: L 129 SER cc_start: 0.5774 (OUTLIER) cc_final: 0.5177 (m) REVERT: L 197 MET cc_start: 0.2991 (tpt) cc_final: 0.2057 (tpp) REVERT: L 504 PHE cc_start: 0.5544 (t80) cc_final: 0.5341 (t80) outliers start: 125 outliers final: 89 residues processed: 428 average time/residue: 0.3544 time to fit residues: 244.1148 Evaluate side-chains 419 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 321 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 262 ILE Chi-restraints excluded: chain L residue 352 ILE Chi-restraints excluded: chain L residue 443 GLU Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.9980 chunk 113 optimal weight: 0.0970 chunk 170 optimal weight: 0.7980 chunk 85 optimal weight: 0.0570 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 194 optimal weight: 0.0040 chunk 141 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 overall best weight: 0.2508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 583 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25556 Z= 0.179 Angle : 0.655 9.290 35283 Z= 0.331 Chirality : 0.043 0.227 4021 Planarity : 0.004 0.055 4095 Dihedral : 20.294 178.844 4839 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.12 % Allowed : 26.19 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.16), residues: 2842 helix: 0.48 (0.17), residues: 1003 sheet: -0.56 (0.24), residues: 443 loop : -0.79 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 258 HIS 0.006 0.001 HIS H 85 PHE 0.026 0.002 PHE L 36 TYR 0.026 0.001 TYR G 99 ARG 0.010 0.000 ARG L 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 364 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8070 (tp30) cc_final: 0.7738 (mm-30) REVERT: A 204 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.5536 (t80) REVERT: C 140 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7100 (tt) REVERT: C 294 ASP cc_start: 0.6647 (t0) cc_final: 0.6300 (t0) REVERT: C 295 TYR cc_start: 0.7904 (m-10) cc_final: 0.7413 (m-80) REVERT: D 89 GLU cc_start: 0.7609 (pp20) cc_final: 0.7015 (pm20) REVERT: F 30 ASN cc_start: 0.8098 (m-40) cc_final: 0.7838 (t0) REVERT: F 168 MET cc_start: 0.2777 (mmm) cc_final: 0.1391 (mmm) REVERT: F 175 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: G 40 LEU cc_start: 0.5571 (OUTLIER) cc_final: 0.5352 (tp) REVERT: G 120 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7610 (mt-10) REVERT: G 264 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6175 (tp) REVERT: H 39 MET cc_start: 0.5582 (mmm) cc_final: 0.4874 (mmt) REVERT: H 62 GLN cc_start: 0.7757 (mp10) cc_final: 0.7460 (mm110) REVERT: H 167 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.5941 (tt) REVERT: L 129 SER cc_start: 0.5041 (OUTLIER) cc_final: 0.4575 (m) REVERT: L 197 MET cc_start: 0.2890 (tpt) cc_final: 0.2454 (tpp) REVERT: L 504 PHE cc_start: 0.5443 (t80) cc_final: 0.5186 (t80) outliers start: 96 outliers final: 73 residues processed: 429 average time/residue: 0.3409 time to fit residues: 235.0315 Evaluate side-chains 417 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 337 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 352 ILE Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 580 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 249 optimal weight: 0.0470 chunk 265 optimal weight: 50.0000 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 208 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 264 optimal weight: 20.0000 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25556 Z= 0.268 Angle : 0.713 19.785 35283 Z= 0.358 Chirality : 0.044 0.357 4021 Planarity : 0.005 0.065 4095 Dihedral : 20.254 179.977 4839 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.25 % Allowed : 26.66 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.16), residues: 2842 helix: 0.44 (0.17), residues: 992 sheet: -0.73 (0.23), residues: 458 loop : -0.84 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 258 HIS 0.007 0.001 HIS D 291 PHE 0.021 0.002 PHE L 36 TYR 0.032 0.002 TYR A 3 ARG 0.008 0.001 ARG L 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 328 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8151 (tp30) cc_final: 0.7789 (mm-30) REVERT: C 140 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6979 (tt) REVERT: C 250 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: C 266 ARG cc_start: 0.7456 (mtm110) cc_final: 0.7209 (mtm-85) REVERT: C 294 ASP cc_start: 0.6731 (t0) cc_final: 0.6423 (t0) REVERT: E 124 MET cc_start: 0.5933 (mmm) cc_final: 0.5539 (mmm) REVERT: E 165 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5861 (mm-30) REVERT: F 30 ASN cc_start: 0.8217 (m-40) cc_final: 0.7921 (t0) REVERT: F 57 ILE cc_start: 0.7803 (mm) cc_final: 0.7590 (pt) REVERT: F 168 MET cc_start: 0.2871 (mmm) cc_final: 0.1735 (mmm) REVERT: F 175 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6440 (tm-30) REVERT: G 40 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5460 (tp) REVERT: G 120 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7587 (mt-10) REVERT: G 160 LEU cc_start: 0.4422 (OUTLIER) cc_final: 0.4033 (pp) REVERT: G 264 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6303 (tp) REVERT: H 62 GLN cc_start: 0.7818 (mp10) cc_final: 0.7573 (mm110) REVERT: H 167 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6033 (tt) REVERT: L 129 SER cc_start: 0.5184 (OUTLIER) cc_final: 0.4776 (m) REVERT: L 197 MET cc_start: 0.2958 (tpt) cc_final: 0.2078 (tpp) REVERT: L 362 MET cc_start: 0.4430 (mmp) cc_final: 0.4224 (mmt) outliers start: 99 outliers final: 83 residues processed: 402 average time/residue: 0.3338 time to fit residues: 216.7972 Evaluate side-chains 407 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 316 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 341 PHE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 352 ILE Chi-restraints excluded: chain L residue 501 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 580 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 HIS L 243 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25556 Z= 0.226 Angle : 0.702 19.177 35283 Z= 0.350 Chirality : 0.044 0.379 4021 Planarity : 0.005 0.060 4095 Dihedral : 20.217 178.510 4839 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.99 % Allowed : 27.39 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.16), residues: 2842 helix: 0.45 (0.17), residues: 994 sheet: -0.75 (0.23), residues: 458 loop : -0.85 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 258 HIS 0.012 0.001 HIS D 291 PHE 0.025 0.002 PHE L 36 TYR 0.035 0.002 TYR G 99 ARG 0.007 0.001 ARG L 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5684 Ramachandran restraints generated. 2842 Oldfield, 0 Emsley, 2842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 330 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.6816 (tmm) cc_final: 0.6550 (tmm) REVERT: C 250 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: C 266 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7189 (mtm-85) REVERT: C 294 ASP cc_start: 0.6578 (t0) cc_final: 0.6206 (t0) REVERT: D 89 GLU cc_start: 0.7554 (pp20) cc_final: 0.6977 (pm20) REVERT: E 124 MET cc_start: 0.5980 (mmm) cc_final: 0.5535 (mmm) REVERT: E 145 MET cc_start: 0.5238 (mmm) cc_final: 0.4912 (mmm) REVERT: E 165 GLU cc_start: 0.6093 (mm-30) cc_final: 0.5755 (mm-30) REVERT: F 30 ASN cc_start: 0.8309 (m-40) cc_final: 0.8039 (t0) REVERT: F 57 ILE cc_start: 0.7789 (mm) cc_final: 0.7584 (pt) REVERT: F 168 MET cc_start: 0.2956 (mmm) cc_final: 0.1871 (mmm) REVERT: F 175 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: G 2 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5791 (tm130) REVERT: G 40 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5557 (tp) REVERT: G 120 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7622 (mt-10) REVERT: G 160 LEU cc_start: 0.4449 (OUTLIER) cc_final: 0.4074 (pp) REVERT: G 264 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6225 (tp) REVERT: H 167 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.5831 (tt) REVERT: L 129 SER cc_start: 0.5014 (OUTLIER) cc_final: 0.4569 (m) REVERT: L 197 MET cc_start: 0.2924 (tpt) cc_final: 0.2016 (tpp) REVERT: L 362 MET cc_start: 0.4464 (mmp) cc_final: 0.4095 (mmm) REVERT: L 562 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6310 (mp0) outliers start: 93 outliers final: 74 residues processed: 396 average time/residue: 0.3339 time to fit residues: 215.2117 Evaluate side-chains 399 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 317 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 207 TRP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 2 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 306 ASN Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 352 ILE Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 580 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 8.9990 chunk 250 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 235 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.139063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.116643 restraints weight = 77019.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.116279 restraints weight = 60257.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.117226 restraints weight = 44275.803| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 25556 Z= 0.299 Angle : 0.823 59.188 35283 Z= 0.439 Chirality : 0.045 0.611 4021 Planarity : 0.005 0.059 4095 Dihedral : 20.215 178.524 4839 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.04 % Allowed : 27.44 % Favored : 68.53 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.16), residues: 2842 helix: 0.45 (0.17), residues: 994 sheet: -0.75 (0.23), residues: 458 loop : -0.85 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 258 HIS 0.029 0.001 HIS C 127 PHE 0.025 0.002 PHE L 36 TYR 0.030 0.002 TYR G 99 ARG 0.007 0.000 ARG L 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5121.32 seconds wall clock time: 94 minutes 24.59 seconds (5664.59 seconds total)