Starting phenix.real_space_refine on Thu Feb 22 08:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3h_12706/02_2024/7o3h_12706_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3h_12706/02_2024/7o3h_12706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3h_12706/02_2024/7o3h_12706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3h_12706/02_2024/7o3h_12706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3h_12706/02_2024/7o3h_12706_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3h_12706/02_2024/7o3h_12706_updated.pdb" } resolution = 2.6 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= 0.014 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 22 5.49 5 S 165 5.16 5 C 21602 2.51 5 N 5687 2.21 5 O 6214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C ASP 374": "OD1" <-> "OD2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "E ASP 9": "OD1" <-> "OD2" Residue "E ASP 20": "OD1" <-> "OD2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 115": "OD1" <-> "OD2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "L PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 407": "OD1" <-> "OD2" Residue "N PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 214": "OD1" <-> "OD2" Residue "N ASP 216": "OD1" <-> "OD2" Residue "N ASP 228": "OD1" <-> "OD2" Residue "N ASP 248": "OD1" <-> "OD2" Residue "O ASP 22": "OD1" <-> "OD2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "P ASP 4": "OD1" <-> "OD2" Residue "P ASP 9": "OD1" <-> "OD2" Residue "P ASP 12": "OD1" <-> "OD2" Residue "P ASP 20": "OD1" <-> "OD2" Residue "P PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 103": "OE1" <-> "OE2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "R TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "S ASP 13": "OD1" <-> "OD2" Residue "S ASP 51": "OD1" <-> "OD2" Residue "S ASP 58": "OD1" <-> "OD2" Residue "U PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 43": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33700 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3466 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "B" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3154 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 408} Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3046 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 357} Chain: "D" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1919 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 218} Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 900 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "G" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 674 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "H" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 563 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "J" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "K" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "L" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3460 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain: "M" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3154 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 408} Chain: "N" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3046 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 357} Chain: "O" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1909 Classifications: {'peptide': 240} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 217} Chain: "P" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "Q" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 894 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "R" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 637 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "S" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 563 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "U" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "V" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 438 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "T" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 554 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 9, 'TRANS': 68} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 82 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'3PE': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "N" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 169 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "O" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'FES': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "R" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12675 SG CYS E 139 85.672 47.390 143.327 1.00170.07 S ATOM 12811 SG CYS E 158 83.776 47.338 146.469 1.00162.86 S ATOM 28809 SG CYS P 139 40.774 84.279 144.186 1.00172.91 S ATOM 28945 SG CYS P 158 42.637 85.385 147.222 1.00155.24 S Time building chain proxies: 18.20, per 1000 atoms: 0.54 Number of scatterers: 33700 At special positions: 0 Unit cell: (127.453, 133.45, 168.437, 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) Fe 10 26.01 S 165 16.00 P 22 15.00 O 6214 8.00 N 5687 7.00 C 21602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS H 38 " - pdb=" SG CYS H 52 " distance=2.02 Simple disulfide: pdb=" SG CYS P 144 " - pdb=" SG CYS P 160 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 66 " distance=2.03 Simple disulfide: pdb=" SG CYS S 38 " - pdb=" SG CYS S 52 " distance=2.04 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 202 " pdb="FE1 FES E 202 " - pdb=" SG CYS E 158 " pdb="FE1 FES E 202 " - pdb=" SG CYS E 139 " pdb=" FES P 201 " pdb="FE2 FES P 201 " - pdb=" NE2 HIS P 161 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 139 " pdb="FE2 FES P 201 " - pdb=" ND1 HIS P 141 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 158 " Number of angles added : 6 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 18 sheets defined 50.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.929A pdb=" N PHE A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 328 through 347 removed outlier: 5.891A pdb=" N ASP A 332 " --> pdb=" O MET A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 372 through 385 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 134 through 153 removed outlier: 4.715A pdb=" N SER B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.635A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 372 Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 419 Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 29 through 52 removed outlier: 4.340A pdb=" N GLY C 34 " --> pdb=" O TRP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 76 through 103 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.306A pdb=" N ALA C 152 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 172 through 201 Proline residue: C 186 - end of helix Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 223 through 243 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 272 through 282 removed outlier: 5.123A pdb=" N PHE C 276 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 306 removed outlier: 5.126A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Proline residue: C 305 - end of helix Processing helix chain 'C' and resid 319 through 339 Processing helix chain 'C' and resid 347 through 363 Processing helix chain 'C' and resid 365 through 376 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 48 through 51 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 198 through 231 Proline residue: D 217 - end of helix removed outlier: 4.992A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 4 No H-bonds generated for 'chain 'E' and resid 2 through 4' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 29 through 61 Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'F' and resid 11 through 24 Processing helix chain 'F' and resid 34 through 36 No H-bonds generated for 'chain 'F' and resid 34 through 36' Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 52 through 70 Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'F' and resid 91 through 109 Processing helix chain 'G' and resid 29 through 69 Proline residue: G 35 - end of helix removed outlier: 5.323A pdb=" N LEU G 46 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Proline residue: G 50 - end of helix Processing helix chain 'H' and resid 14 through 23 Processing helix chain 'H' and resid 26 through 43 Processing helix chain 'H' and resid 54 through 70 removed outlier: 3.830A pdb=" N LYS H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'J' and resid 5 through 12 Processing helix chain 'J' and resid 17 through 46 Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'K' and resid 8 through 36 Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 39 through 42 No H-bonds generated for 'chain 'K' and resid 39 through 42' Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.812A pdb=" N GLY K 50 " --> pdb=" O TYR K 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 45 through 47 No H-bonds generated for 'chain 'L' and resid 45 through 47' Processing helix chain 'L' and resid 55 through 62 Processing helix chain 'L' and resid 74 through 80 Processing helix chain 'L' and resid 106 through 116 Processing helix chain 'L' and resid 124 through 143 removed outlier: 4.167A pdb=" N ALA L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 157 Processing helix chain 'L' and resid 171 through 176 Processing helix chain 'L' and resid 179 through 189 Processing helix chain 'L' and resid 192 through 194 No H-bonds generated for 'chain 'L' and resid 192 through 194' Processing helix chain 'L' and resid 205 through 215 Processing helix chain 'L' and resid 265 through 277 Processing helix chain 'L' and resid 287 through 289 No H-bonds generated for 'chain 'L' and resid 287 through 289' Processing helix chain 'L' and resid 293 through 300 Processing helix chain 'L' and resid 328 through 347 removed outlier: 5.650A pdb=" N ASP L 332 " --> pdb=" O MET L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 368 Processing helix chain 'L' and resid 372 through 385 Processing helix chain 'L' and resid 392 through 400 Processing helix chain 'L' and resid 404 through 414 Processing helix chain 'L' and resid 434 through 440 Processing helix chain 'M' and resid 55 through 57 No H-bonds generated for 'chain 'M' and resid 55 through 57' Processing helix chain 'M' and resid 65 through 71 Processing helix chain 'M' and resid 82 through 92 Processing helix chain 'M' and resid 113 through 128 removed outlier: 3.504A pdb=" N ILE M 116 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU M 117 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE M 118 " --> pdb=" O ASP M 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU M 124 " --> pdb=" O GLU M 121 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 128 " --> pdb=" O ASN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 153 removed outlier: 4.824A pdb=" N SER M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 167 Processing helix chain 'M' and resid 188 through 198 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 213 through 223 Processing helix chain 'M' and resid 267 through 279 Processing helix chain 'M' and resid 294 through 302 removed outlier: 3.897A pdb=" N LYS M 301 " --> pdb=" O GLN M 297 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY M 302 " --> pdb=" O SER M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 348 Processing helix chain 'M' and resid 354 through 371 Processing helix chain 'M' and resid 375 through 388 Processing helix chain 'M' and resid 395 through 403 Processing helix chain 'M' and resid 407 through 419 Processing helix chain 'N' and resid 4 through 6 No H-bonds generated for 'chain 'N' and resid 4 through 6' Processing helix chain 'N' and resid 9 through 18 removed outlier: 3.996A pdb=" N ILE N 13 " --> pdb=" O PRO N 9 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 53 removed outlier: 4.435A pdb=" N GLY N 34 " --> pdb=" O TRP N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 71 Processing helix chain 'N' and resid 76 through 103 Processing helix chain 'N' and resid 106 through 108 No H-bonds generated for 'chain 'N' and resid 106 through 108' Processing helix chain 'N' and resid 110 through 133 Processing helix chain 'N' and resid 137 through 151 Processing helix chain 'N' and resid 157 through 165 Processing helix chain 'N' and resid 172 through 203 Proline residue: N 186 - end of helix Processing helix chain 'N' and resid 223 through 244 Processing helix chain 'N' and resid 253 through 256 Processing helix chain 'N' and resid 272 through 283 removed outlier: 5.227A pdb=" N PHE N 276 " --> pdb=" O TYR N 273 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU N 281 " --> pdb=" O TYR N 278 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG N 282 " --> pdb=" O ALA N 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER N 283 " --> pdb=" O ILE N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 307 Proline residue: N 305 - end of helix Processing helix chain 'N' and resid 319 through 340 removed outlier: 3.762A pdb=" N GLY N 340 " --> pdb=" O THR N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 363 Processing helix chain 'N' and resid 365 through 376 Processing helix chain 'O' and resid 23 through 35 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 58 through 66 Processing helix chain 'O' and resid 98 through 104 Processing helix chain 'O' and resid 124 through 131 Processing helix chain 'O' and resid 179 through 194 Processing helix chain 'O' and resid 198 through 231 Proline residue: O 217 - end of helix removed outlier: 4.724A pdb=" N VAL O 229 " --> pdb=" O HIS O 225 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU O 230 " --> pdb=" O LYS O 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 4 No H-bonds generated for 'chain 'P' and resid 2 through 4' Processing helix chain 'P' and resid 16 through 18 No H-bonds generated for 'chain 'P' and resid 16 through 18' Processing helix chain 'P' and resid 29 through 62 Processing helix chain 'P' and resid 66 through 72 Processing helix chain 'P' and resid 103 through 111 removed outlier: 3.896A pdb=" N ALA P 111 " --> pdb=" O ASP P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 126 No H-bonds generated for 'chain 'P' and resid 123 through 126' Processing helix chain 'Q' and resid 11 through 24 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 41 through 48 Processing helix chain 'Q' and resid 52 through 70 Processing helix chain 'Q' and resid 77 through 79 No H-bonds generated for 'chain 'Q' and resid 77 through 79' Processing helix chain 'Q' and resid 83 through 85 No H-bonds generated for 'chain 'Q' and resid 83 through 85' Processing helix chain 'Q' and resid 91 through 109 Processing helix chain 'R' and resid 29 through 70 Proline residue: R 35 - end of helix removed outlier: 5.178A pdb=" N LEU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) Proline residue: R 50 - end of helix Processing helix chain 'S' and resid 14 through 23 Processing helix chain 'S' and resid 26 through 43 removed outlier: 3.542A pdb=" N LYS S 30 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 70 removed outlier: 3.515A pdb=" N LYS S 70 " --> pdb=" O CYS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 74 No H-bonds generated for 'chain 'S' and resid 72 through 74' Processing helix chain 'U' and resid 5 through 12 Processing helix chain 'U' and resid 17 through 46 Processing helix chain 'U' and resid 52 through 54 No H-bonds generated for 'chain 'U' and resid 52 through 54' Processing helix chain 'U' and resid 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'V' and resid 8 through 35 Proline residue: V 19 - end of helix Processing helix chain 'V' and resid 39 through 42 No H-bonds generated for 'chain 'V' and resid 39 through 42' Processing helix chain 'V' and resid 47 through 51 removed outlier: 4.128A pdb=" N GLY V 50 " --> pdb=" O TYR V 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 7 No H-bonds generated for 'chain 'T' and resid 4 through 7' Processing helix chain 'T' and resid 10 through 15 Proline residue: T 13 - end of helix No H-bonds generated for 'chain 'T' and resid 10 through 15' Processing helix chain 'T' and resid 52 through 55 No H-bonds generated for 'chain 'T' and resid 52 through 55' Processing sheet with id= A, first strand: chain 'A' and resid 15 through 18 Processing sheet with id= B, first strand: chain 'A' and resid 239 through 244 Processing sheet with id= C, first strand: chain 'B' and resid 25 through 28 Processing sheet with id= D, first strand: chain 'B' and resid 242 through 247 removed outlier: 3.638A pdb=" N GLY B 320 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 22 through 24 Processing sheet with id= F, first strand: chain 'D' and resid 69 through 72 Processing sheet with id= G, first strand: chain 'E' and resid 86 through 91 Processing sheet with id= H, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= I, first strand: chain 'E' and resid 185 through 187 Processing sheet with id= J, first strand: chain 'L' and resid 15 through 18 Processing sheet with id= K, first strand: chain 'L' and resid 239 through 244 Processing sheet with id= L, first strand: chain 'M' and resid 25 through 28 Processing sheet with id= M, first strand: chain 'M' and resid 242 through 247 removed outlier: 3.558A pdb=" N GLY M 242 " --> pdb=" O LYS M 422 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 22 through 24 Processing sheet with id= O, first strand: chain 'O' and resid 69 through 72 Processing sheet with id= P, first strand: chain 'P' and resid 86 through 91 Processing sheet with id= Q, first strand: chain 'P' and resid 156 through 158 Processing sheet with id= R, first strand: chain 'T' and resid 65 through 67 1657 hydrogen bonds defined for protein. 4488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.56 Time building geometry restraints manager: 14.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 14122 1.40 - 1.60: 20097 1.60 - 1.80: 247 1.80 - 2.01: 31 2.01 - 2.21: 23 Bond restraints: 34520 Sorted by residual: bond pdb=" OB3 CDL A 502 " pdb=" PB2 CDL A 502 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.00e-02 1.00e+04 2.66e+01 bond pdb=" OB3 CDL N 404 " pdb=" PB2 CDL N 404 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.00e-02 1.00e+04 2.66e+01 bond pdb=" OB3 CDL R 101 " pdb=" PB2 CDL R 101 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.59e+01 bond pdb=" OB3 CDL G 101 " pdb=" PB2 CDL G 101 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.55e+01 bond pdb=" OB3 CDL G 102 " pdb=" PB2 CDL G 102 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.54e+01 ... (remaining 34515 not shown) Histogram of bond angle deviations from ideal: 74.92 - 95.79: 28 95.79 - 116.67: 23447 116.67 - 137.54: 23331 137.54 - 158.42: 0 158.42 - 179.29: 12 Bond angle restraints: 46818 Sorted by residual: angle pdb=" CA LEU E 78 " pdb=" CB LEU E 78 " pdb=" CG LEU E 78 " ideal model delta sigma weight residual 116.30 134.17 -17.87 3.50e+00 8.16e-02 2.61e+01 angle pdb=" N GLU M 121 " pdb=" CA GLU M 121 " pdb=" CB GLU M 121 " ideal model delta sigma weight residual 110.28 117.85 -7.57 1.55e+00 4.16e-01 2.39e+01 angle pdb=" N ALA G 49 " pdb=" CA ALA G 49 " pdb=" C ALA G 49 " ideal model delta sigma weight residual 113.16 119.94 -6.78 1.42e+00 4.96e-01 2.28e+01 angle pdb=" CB MET N 138 " pdb=" CG MET N 138 " pdb=" SD MET N 138 " ideal model delta sigma weight residual 112.70 126.26 -13.56 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C SER L 220 " pdb=" N ARG L 221 " pdb=" CA ARG L 221 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.83e+01 ... (remaining 46813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.21: 19514 25.21 - 50.42: 926 50.42 - 75.62: 180 75.62 - 100.83: 39 100.83 - 126.04: 3 Dihedral angle restraints: 20662 sinusoidal: 8589 harmonic: 12073 Sorted by residual: dihedral pdb=" C2B HEM N 402 " pdb=" C3B HEM N 402 " pdb=" CAB HEM N 402 " pdb=" CBB HEM N 402 " ideal model delta sinusoidal sigma weight residual -0.00 -82.82 82.82 2 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" C2B HEM C 402 " pdb=" C3B HEM C 402 " pdb=" CAB HEM C 402 " pdb=" CBB HEM C 402 " ideal model delta sinusoidal sigma weight residual 0.00 -80.92 80.92 2 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" C2C HEM N 401 " pdb=" C3C HEM N 401 " pdb=" CAC HEM N 401 " pdb=" CBC HEM N 401 " ideal model delta sinusoidal sigma weight residual 0.00 -75.96 75.96 2 1.00e+01 1.00e-02 4.52e+01 ... (remaining 20659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4717 0.102 - 0.205: 321 0.205 - 0.307: 9 0.307 - 0.409: 1 0.409 - 0.512: 4 Chirality restraints: 5052 Sorted by residual: chirality pdb=" C2 3PE R 102 " pdb=" C1 3PE R 102 " pdb=" C3 3PE R 102 " pdb=" O21 3PE R 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.01 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA4 CDL R 101 " pdb=" CA3 CDL R 101 " pdb=" CA6 CDL R 101 " pdb=" OA6 CDL R 101 " both_signs ideal model delta sigma weight residual False -2.57 -2.09 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CB4 CDL N 404 " pdb=" CB3 CDL N 404 " pdb=" CB6 CDL N 404 " pdb=" OB6 CDL N 404 " both_signs ideal model delta sigma weight residual False -2.57 -2.12 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 5049 not shown) Planarity restraints: 5935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 303 " 0.021 2.00e-02 2.50e+03 5.94e-02 7.94e+01 pdb=" C2C HEC O 303 " -0.163 2.00e-02 2.50e+03 pdb=" C3C HEC O 303 " 0.024 2.00e-02 2.50e+03 pdb=" C4C HEC O 303 " 0.002 2.00e-02 2.50e+03 pdb=" CAC HEC O 303 " 0.032 2.00e-02 2.50e+03 pdb=" CHC HEC O 303 " 0.029 2.00e-02 2.50e+03 pdb=" CHD HEC O 303 " -0.003 2.00e-02 2.50e+03 pdb=" CMC HEC O 303 " 0.048 2.00e-02 2.50e+03 pdb=" NC HEC O 303 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 301 " -0.021 2.00e-02 2.50e+03 5.91e-02 7.86e+01 pdb=" C2C HEC D 301 " 0.162 2.00e-02 2.50e+03 pdb=" C3C HEC D 301 " -0.024 2.00e-02 2.50e+03 pdb=" C4C HEC D 301 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC D 301 " -0.032 2.00e-02 2.50e+03 pdb=" CHC HEC D 301 " -0.029 2.00e-02 2.50e+03 pdb=" CHD HEC D 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC D 301 " -0.048 2.00e-02 2.50e+03 pdb=" NC HEC D 301 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 183 " -0.009 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE N 183 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE N 183 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE N 183 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE N 183 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 183 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE N 183 " 0.003 2.00e-02 2.50e+03 ... (remaining 5932 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 370 2.63 - 3.20: 28325 3.20 - 3.77: 55126 3.77 - 4.33: 76536 4.33 - 4.90: 124044 Nonbonded interactions: 284401 Sorted by model distance: nonbonded pdb=" NE2 HIS C 83 " pdb="FE HEM C 401 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 182 " pdb="FE HEM N 401 " model vdw 2.070 3.080 nonbonded pdb=" NE2 HIS N 97 " pdb="FE HEM N 402 " model vdw 2.202 3.080 nonbonded pdb=" SD MET D 160 " pdb="FE HEC D 301 " model vdw 2.209 3.360 nonbonded pdb=" SD MET O 160 " pdb="FE HEC O 303 " model vdw 2.211 3.360 ... (remaining 284396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 446 or resid 501)) selection = (chain 'L' and (resid 2 through 445 or (resid 446 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 501)) } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = (chain 'N' and (resid 1 through 380 or resid 401 through 402 or (resid 403 and ( \ name N or name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) } ncs_group { reference = (chain 'D' and resid 1 through 240) selection = (chain 'O' and resid 1 through 240) } ncs_group { reference = (chain 'E' and resid 1 through 196) selection = (chain 'P' and resid 1 through 196) } ncs_group { reference = (chain 'F' and resid 10 through 110) selection = chain 'Q' } ncs_group { reference = (chain 'G' and (resid 1 through 76 or (resid 102 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C32 or \ name C33 or name C51 or name C52 or name C71 or name C72 or name CA2 or name CA \ 3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 or nam \ e CB6 or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or \ name OA6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name OB6 \ or name OB7 or name OB8 or name OB9 or name PA1 or name PB2)) or resid 103)) selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = (chain 'J' and resid 2 through 61) selection = chain 'U' } ncs_group { reference = chain 'K' selection = (chain 'V' and resid 2 through 52) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.950 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 92.480 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.320 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 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 : 0.006 0.082 34520 Z= 0.369 Angle : 0.882 17.867 46818 Z= 0.459 Chirality : 0.054 0.512 5052 Planarity : 0.007 0.083 5935 Dihedral : 15.256 126.039 12881 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: -0.68 (0.12), residues: 4119 helix: -0.36 (0.10), residues: 2093 sheet: 0.81 (0.26), residues: 380 loop : -0.70 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 135 HIS 0.009 0.001 HIS N 196 PHE 0.054 0.002 PHE N 183 TYR 0.031 0.002 TYR F 55 ARG 0.006 0.000 ARG M 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 3.868 Fit side-chains REVERT: B 218 GLN cc_start: 0.8415 (pt0) cc_final: 0.8202 (pt0) REVERT: B 246 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8468 (mm-30) REVERT: C 111 GLU cc_start: 0.8485 (mp0) cc_final: 0.8238 (mt-10) REVERT: D 77 ASP cc_start: 0.7968 (p0) cc_final: 0.7248 (p0) REVERT: E 23 LYS cc_start: 0.8607 (tttm) cc_final: 0.8280 (tttp) REVERT: F 42 ASP cc_start: 0.8109 (m-30) cc_final: 0.7765 (m-30) REVERT: F 96 GLU cc_start: 0.8362 (tp30) cc_final: 0.8091 (pt0) REVERT: J 48 GLU cc_start: 0.8182 (pm20) cc_final: 0.7977 (pm20) REVERT: L 115 ASP cc_start: 0.7349 (t70) cc_final: 0.6777 (t70) REVERT: M 218 GLN cc_start: 0.8239 (pp30) cc_final: 0.8034 (pp30) REVERT: P 135 LEU cc_start: 0.7504 (mt) cc_final: 0.7174 (pp) REVERT: T 47 ARG cc_start: 0.8328 (ptp-110) cc_final: 0.7698 (ttm-80) outliers start: 0 outliers final: 1 residues processed: 687 average time/residue: 1.6817 time to fit residues: 1345.9306 Evaluate side-chains 511 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 510 time to evaluate : 3.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 251 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 166 optimal weight: 40.0000 chunk 321 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 195 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 372 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN A 146 GLN A 400 GLN A 430 GLN A 435 ASN C 201 HIS ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN F 73 GLN G 73 ASN K 16 ASN L 6 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 ASN V 16 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34520 Z= 0.311 Angle : 0.643 15.117 46818 Z= 0.319 Chirality : 0.044 0.256 5052 Planarity : 0.005 0.064 5935 Dihedral : 12.361 131.242 5162 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.33 % Allowed : 10.79 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 0.57 (0.13), residues: 4119 helix: 0.88 (0.11), residues: 2101 sheet: 0.69 (0.26), residues: 385 loop : -0.24 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 141 HIS 0.010 0.001 HIS D 225 PHE 0.020 0.002 PHE C 183 TYR 0.025 0.002 TYR N 81 ARG 0.007 0.001 ARG U 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 518 time to evaluate : 3.925 Fit side-chains REVERT: C 111 GLU cc_start: 0.8674 (mp0) cc_final: 0.8419 (mt-10) REVERT: C 271 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8467 (mt-10) REVERT: E 23 LYS cc_start: 0.8639 (tttm) cc_final: 0.8411 (tttp) REVERT: E 87 MET cc_start: 0.5962 (ptm) cc_final: 0.5555 (ptt) REVERT: F 42 ASP cc_start: 0.8181 (m-30) cc_final: 0.7956 (m-30) REVERT: F 96 GLU cc_start: 0.8482 (tp30) cc_final: 0.8130 (pt0) REVERT: F 110 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8102 (pttp) REVERT: H 50 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: J 48 GLU cc_start: 0.8302 (pm20) cc_final: 0.8040 (pm20) REVERT: L 381 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8373 (ttm110) REVERT: M 110 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8611 (tm-30) REVERT: M 218 GLN cc_start: 0.8356 (pp30) cc_final: 0.8115 (pp30) REVERT: N 377 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8807 (mp) REVERT: P 135 LEU cc_start: 0.7735 (mt) cc_final: 0.7496 (pp) REVERT: Q 32 MET cc_start: 0.9255 (mmm) cc_final: 0.9049 (mtp) REVERT: Q 101 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8395 (tmm160) REVERT: U 16 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7888 (mmm160) outliers start: 82 outliers final: 31 residues processed: 557 average time/residue: 1.6317 time to fit residues: 1065.7778 Evaluate side-chains 526 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 489 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain L residue 367 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 253 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 402 optimal weight: 20.0000 chunk 332 optimal weight: 30.0000 chunk 369 optimal weight: 0.2980 chunk 127 optimal weight: 7.9990 chunk 299 optimal weight: 20.0000 overall best weight: 6.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN A 400 GLN F 73 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 270 ASN O 71 GLN V 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34520 Z= 0.256 Angle : 0.598 14.387 46818 Z= 0.295 Chirality : 0.043 0.256 5052 Planarity : 0.004 0.061 5935 Dihedral : 11.846 137.547 5162 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.70 % Allowed : 12.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 0.97 (0.13), residues: 4119 helix: 1.26 (0.11), residues: 2101 sheet: 0.76 (0.26), residues: 385 loop : -0.08 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 141 HIS 0.008 0.001 HIS D 225 PHE 0.018 0.001 PHE Q 60 TYR 0.019 0.001 TYR N 224 ARG 0.009 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 511 time to evaluate : 4.004 Fit side-chains revert: symmetry clash REVERT: C 111 GLU cc_start: 0.8672 (mp0) cc_final: 0.8415 (mt-10) REVERT: C 271 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8463 (mt-10) REVERT: E 23 LYS cc_start: 0.8642 (tttm) cc_final: 0.8357 (tttp) REVERT: E 87 MET cc_start: 0.5986 (ptm) cc_final: 0.5603 (ptt) REVERT: F 42 ASP cc_start: 0.8214 (m-30) cc_final: 0.7977 (m-30) REVERT: F 96 GLU cc_start: 0.8503 (tp30) cc_final: 0.8155 (pt0) REVERT: L 42 ASP cc_start: 0.8890 (t0) cc_final: 0.8546 (t70) REVERT: M 110 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8632 (tm-30) REVERT: M 218 GLN cc_start: 0.8400 (pp30) cc_final: 0.8144 (pp30) REVERT: N 1 MET cc_start: 0.7358 (ttt) cc_final: 0.7143 (ttp) REVERT: N 344 GLU cc_start: 0.7984 (mp0) cc_final: 0.7706 (mp0) REVERT: P 135 LEU cc_start: 0.7789 (mt) cc_final: 0.7588 (pp) REVERT: Q 91 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8694 (tm-30) REVERT: Q 95 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8932 (mttm) REVERT: Q 101 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8240 (tmm160) REVERT: U 16 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7947 (mmm160) outliers start: 95 outliers final: 41 residues processed: 558 average time/residue: 1.6526 time to fit residues: 1077.8935 Evaluate side-chains 533 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 487 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 0.0980 chunk 280 optimal weight: 9.9990 chunk 193 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 250 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 chunk 396 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 354 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 400 GLN C 32 ASN D 71 GLN F 73 GLN G 36 ASN G 73 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 289 ASN ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN V 16 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34520 Z= 0.201 Angle : 0.561 13.429 46818 Z= 0.277 Chirality : 0.041 0.244 5052 Planarity : 0.004 0.055 5935 Dihedral : 11.504 144.111 5160 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.73 % Allowed : 13.46 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.22 (0.13), residues: 4119 helix: 1.47 (0.11), residues: 2098 sheet: 0.85 (0.26), residues: 382 loop : 0.04 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 141 HIS 0.007 0.001 HIS D 225 PHE 0.017 0.001 PHE Q 60 TYR 0.016 0.001 TYR N 224 ARG 0.012 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 527 time to evaluate : 4.317 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8564 (mt0) REVERT: B 223 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: C 111 GLU cc_start: 0.8641 (mp0) cc_final: 0.8380 (mt-10) REVERT: C 271 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8458 (mt-10) REVERT: E 23 LYS cc_start: 0.8644 (tttm) cc_final: 0.8388 (tttp) REVERT: E 87 MET cc_start: 0.5912 (ptm) cc_final: 0.5542 (ptt) REVERT: F 42 ASP cc_start: 0.8219 (m-30) cc_final: 0.7966 (m-30) REVERT: F 96 GLU cc_start: 0.8411 (tp30) cc_final: 0.8151 (pt0) REVERT: L 42 ASP cc_start: 0.8842 (t0) cc_final: 0.8482 (t70) REVERT: M 110 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: N 12 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8642 (ptmm) REVERT: N 343 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8500 (m) REVERT: P 87 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.2859 (pp-130) REVERT: Q 101 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8216 (tmm160) REVERT: U 16 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7893 (mmm160) outliers start: 96 outliers final: 40 residues processed: 576 average time/residue: 1.6630 time to fit residues: 1121.4413 Evaluate side-chains 533 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 485 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 6.9990 chunk 224 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 295 optimal weight: 0.0040 chunk 163 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 273 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 202 optimal weight: 4.9990 chunk 355 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN D 71 GLN F 73 GLN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 218 GLN M 289 ASN ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN Q 73 GLN V 16 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34520 Z= 0.210 Angle : 0.563 13.610 46818 Z= 0.278 Chirality : 0.041 0.245 5052 Planarity : 0.004 0.053 5935 Dihedral : 11.389 147.774 5160 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.59 % Allowed : 14.77 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.33 (0.13), residues: 4119 helix: 1.58 (0.11), residues: 2091 sheet: 0.86 (0.26), residues: 383 loop : 0.08 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 141 HIS 0.007 0.001 HIS D 225 PHE 0.016 0.001 PHE Q 60 TYR 0.016 0.001 TYR N 224 ARG 0.014 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 503 time to evaluate : 4.384 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8524 (mt0) REVERT: B 223 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: C 111 GLU cc_start: 0.8639 (mp0) cc_final: 0.8385 (mt-10) REVERT: C 271 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8464 (mm-30) REVERT: E 23 LYS cc_start: 0.8639 (tttm) cc_final: 0.8399 (tttp) REVERT: E 87 MET cc_start: 0.5878 (ptm) cc_final: 0.5529 (ptt) REVERT: F 42 ASP cc_start: 0.8230 (m-30) cc_final: 0.7979 (m-30) REVERT: F 96 GLU cc_start: 0.8439 (tp30) cc_final: 0.8147 (pt0) REVERT: L 333 ASP cc_start: 0.8871 (m-30) cc_final: 0.8615 (t0) REVERT: M 110 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8622 (tm-30) REVERT: P 135 LEU cc_start: 0.8132 (pp) cc_final: 0.7127 (mt) REVERT: Q 101 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8229 (tmm160) REVERT: S 11 LEU cc_start: 0.8174 (tt) cc_final: 0.7758 (tp) REVERT: U 16 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7901 (mmm160) REVERT: V 39 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5994 (mpp-170) outliers start: 91 outliers final: 44 residues processed: 550 average time/residue: 1.6519 time to fit residues: 1064.5130 Evaluate side-chains 538 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 488 time to evaluate : 3.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 20.0000 chunk 356 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 232 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 208 optimal weight: 20.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN F 73 GLN G 36 ASN G 73 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN M 218 GLN N 331 ASN O 71 GLN Q 73 GLN V 16 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 34520 Z= 0.375 Angle : 0.658 15.781 46818 Z= 0.325 Chirality : 0.045 0.271 5052 Planarity : 0.005 0.059 5935 Dihedral : 11.769 145.881 5160 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.27 % Allowed : 14.80 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.22 (0.13), residues: 4119 helix: 1.46 (0.11), residues: 2089 sheet: 0.86 (0.25), residues: 384 loop : 0.07 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 141 HIS 0.010 0.001 HIS N 196 PHE 0.022 0.002 PHE N 33 TYR 0.024 0.002 TYR N 224 ARG 0.016 0.001 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 499 time to evaluate : 4.042 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: B 223 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: C 111 GLU cc_start: 0.8702 (mp0) cc_final: 0.8409 (mt-10) REVERT: C 271 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8495 (mm-30) REVERT: E 23 LYS cc_start: 0.8643 (tttm) cc_final: 0.8418 (tttm) REVERT: E 87 MET cc_start: 0.5862 (ptm) cc_final: 0.5509 (ptt) REVERT: F 42 ASP cc_start: 0.8292 (m-30) cc_final: 0.8023 (m-30) REVERT: F 96 GLU cc_start: 0.8472 (tp30) cc_final: 0.8176 (pt0) REVERT: M 44 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (mp) REVERT: M 110 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: M 218 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: N 1 MET cc_start: 0.7340 (ttt) cc_final: 0.7080 (ttp) REVERT: P 135 LEU cc_start: 0.8216 (pp) cc_final: 0.7159 (mt) REVERT: Q 101 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8298 (tmm160) REVERT: S 11 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7988 (tp) REVERT: T 62 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8030 (mtt180) outliers start: 115 outliers final: 56 residues processed: 565 average time/residue: 1.6450 time to fit residues: 1088.9706 Evaluate side-chains 546 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 483 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 367 SER Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 335 GLU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 289 optimal weight: 20.0000 chunk 224 optimal weight: 0.0570 chunk 333 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 395 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN C 32 ASN D 71 GLN F 73 GLN G 36 ASN G 73 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN M 218 GLN N 331 ASN O 71 GLN Q 73 GLN V 16 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34520 Z= 0.193 Angle : 0.576 13.135 46818 Z= 0.284 Chirality : 0.041 0.236 5052 Planarity : 0.004 0.061 5935 Dihedral : 11.384 149.735 5160 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.62 % Allowed : 16.25 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.39 (0.13), residues: 4119 helix: 1.59 (0.11), residues: 2093 sheet: 0.90 (0.26), residues: 381 loop : 0.17 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 135 HIS 0.006 0.001 HIS D 225 PHE 0.017 0.001 PHE Q 60 TYR 0.014 0.001 TYR N 81 ARG 0.016 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 507 time to evaluate : 4.298 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8464 (mt0) REVERT: B 223 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: C 111 GLU cc_start: 0.8643 (mp0) cc_final: 0.8386 (mt-10) REVERT: E 23 LYS cc_start: 0.8638 (tttm) cc_final: 0.8437 (tttp) REVERT: E 87 MET cc_start: 0.5814 (ptm) cc_final: 0.5490 (ptt) REVERT: F 42 ASP cc_start: 0.8282 (m-30) cc_final: 0.8006 (m-30) REVERT: F 96 GLU cc_start: 0.8426 (tp30) cc_final: 0.8157 (pt0) REVERT: L 9 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8342 (tp40) REVERT: M 44 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8637 (mp) REVERT: M 110 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: M 218 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8461 (pp30) REVERT: N 1 MET cc_start: 0.7238 (ttt) cc_final: 0.7034 (ttp) REVERT: P 135 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7167 (mt) REVERT: Q 101 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8238 (tmm160) REVERT: U 16 ARG cc_start: 0.8276 (mtm110) cc_final: 0.7847 (mmm160) REVERT: V 39 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5807 (mpp-170) REVERT: T 62 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8036 (mtt180) outliers start: 92 outliers final: 42 residues processed: 554 average time/residue: 1.6665 time to fit residues: 1084.4363 Evaluate side-chains 546 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 495 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 335 GLU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 195 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 310 optimal weight: 20.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN B 343 GLN C 32 ASN F 73 GLN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN N 331 ASN O 71 GLN Q 73 GLN V 16 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 34520 Z= 0.367 Angle : 0.670 15.701 46818 Z= 0.329 Chirality : 0.045 0.260 5052 Planarity : 0.005 0.071 5935 Dihedral : 11.702 147.539 5160 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.82 % Allowed : 16.28 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.27 (0.13), residues: 4119 helix: 1.47 (0.11), residues: 2096 sheet: 0.88 (0.26), residues: 384 loop : 0.14 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 141 HIS 0.009 0.001 HIS C 196 PHE 0.021 0.002 PHE N 33 TYR 0.023 0.002 TYR N 224 ARG 0.019 0.001 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 494 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: B 223 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: C 111 GLU cc_start: 0.8703 (mp0) cc_final: 0.8408 (mt-10) REVERT: E 23 LYS cc_start: 0.8637 (tttm) cc_final: 0.8421 (tttm) REVERT: E 87 MET cc_start: 0.5818 (ptm) cc_final: 0.5483 (ptt) REVERT: F 42 ASP cc_start: 0.8309 (m-30) cc_final: 0.8044 (m-30) REVERT: F 96 GLU cc_start: 0.8459 (tp30) cc_final: 0.8175 (pt0) REVERT: L 9 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8339 (tp40) REVERT: M 25 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8200 (pt0) REVERT: M 44 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8671 (mp) REVERT: M 110 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: N 1 MET cc_start: 0.7354 (ttt) cc_final: 0.7096 (ttp) REVERT: P 135 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7182 (mt) REVERT: Q 101 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8299 (tmm160) REVERT: U 16 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7942 (mmm160) REVERT: T 62 ARG cc_start: 0.8435 (mmm160) cc_final: 0.8060 (mtt180) outliers start: 99 outliers final: 58 residues processed: 547 average time/residue: 1.7094 time to fit residues: 1096.1953 Evaluate side-chains 551 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 485 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 335 GLU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 30.0000 chunk 378 optimal weight: 3.9990 chunk 345 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 160 optimal weight: 0.0370 chunk 289 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 348 optimal weight: 10.0000 chunk 366 optimal weight: 50.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN D 71 GLN F 73 GLN G 36 ASN G 73 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN N 331 ASN O 71 GLN Q 73 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34520 Z= 0.191 Angle : 0.588 12.874 46818 Z= 0.290 Chirality : 0.041 0.225 5052 Planarity : 0.004 0.073 5935 Dihedral : 11.296 151.013 5160 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.16 % Allowed : 17.36 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.42 (0.13), residues: 4119 helix: 1.60 (0.11), residues: 2096 sheet: 0.87 (0.26), residues: 383 loop : 0.22 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 135 HIS 0.006 0.001 HIS D 225 PHE 0.017 0.001 PHE Q 60 TYR 0.013 0.001 TYR N 81 ARG 0.019 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 513 time to evaluate : 3.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: C 111 GLU cc_start: 0.8643 (mp0) cc_final: 0.8386 (mt-10) REVERT: E 87 MET cc_start: 0.5826 (ptm) cc_final: 0.5500 (ptt) REVERT: F 42 ASP cc_start: 0.8280 (m-30) cc_final: 0.8014 (m-30) REVERT: F 96 GLU cc_start: 0.8420 (tp30) cc_final: 0.8154 (pt0) REVERT: L 9 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: M 25 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: M 44 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8616 (mp) REVERT: M 110 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: P 87 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.2996 (pp-130) REVERT: P 135 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7169 (mt) REVERT: Q 101 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8269 (tmm160) REVERT: U 16 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7920 (mmm160) REVERT: V 39 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5710 (mpp-170) REVERT: T 62 ARG cc_start: 0.8401 (mmm160) cc_final: 0.8039 (mtt180) outliers start: 76 outliers final: 47 residues processed: 550 average time/residue: 1.6362 time to fit residues: 1053.9784 Evaluate side-chains 548 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 492 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 335 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 408 optimal weight: 6.9990 chunk 375 optimal weight: 0.0670 chunk 325 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 71 GLN V 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34520 Z= 0.227 Angle : 0.604 13.627 46818 Z= 0.298 Chirality : 0.042 0.229 5052 Planarity : 0.004 0.085 5935 Dihedral : 11.254 150.640 5160 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.91 % Allowed : 18.05 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.44 (0.13), residues: 4119 helix: 1.61 (0.11), residues: 2098 sheet: 0.89 (0.26), residues: 383 loop : 0.23 (0.17), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 135 HIS 0.007 0.001 HIS D 225 PHE 0.016 0.001 PHE Q 60 TYR 0.016 0.001 TYR N 81 ARG 0.020 0.000 ARG J 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 497 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: C 111 GLU cc_start: 0.8644 (mp0) cc_final: 0.8389 (mt-10) REVERT: E 23 LYS cc_start: 0.8532 (tptp) cc_final: 0.8317 (tmtp) REVERT: E 87 MET cc_start: 0.5835 (ptm) cc_final: 0.5513 (ptt) REVERT: F 42 ASP cc_start: 0.8287 (m-30) cc_final: 0.7994 (m-30) REVERT: F 96 GLU cc_start: 0.8441 (tp30) cc_final: 0.8162 (pt0) REVERT: L 9 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8322 (tp40) REVERT: M 25 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: M 44 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8607 (mp) REVERT: M 110 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: O 80 MET cc_start: 0.8662 (mmt) cc_final: 0.8455 (mmp) REVERT: P 87 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.2994 (pp-130) REVERT: P 135 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7171 (mt) REVERT: Q 101 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8258 (tmm160) REVERT: U 16 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7939 (mmm160) REVERT: T 62 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8042 (mtt180) outliers start: 67 outliers final: 48 residues processed: 530 average time/residue: 1.6851 time to fit residues: 1050.3880 Evaluate side-chains 535 residues out of total 3513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 479 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 25 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 335 GLU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 360 SER Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 299 optimal weight: 9.9990 chunk 48 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 325 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 334 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN D 71 GLN G 36 ASN G 73 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 218 GLN N 331 ASN O 71 GLN V 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.081098 restraints weight = 53522.885| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.93 r_work: 0.2925 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34520 Z= 0.199 Angle : 0.596 13.468 46818 Z= 0.293 Chirality : 0.041 0.225 5052 Planarity : 0.004 0.084 5935 Dihedral : 11.151 151.024 5160 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.82 % Allowed : 18.22 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.13), residues: 4119 helix: 1.62 (0.11), residues: 2101 sheet: 0.92 (0.26), residues: 381 loop : 0.24 (0.17), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 135 HIS 0.007 0.001 HIS D 225 PHE 0.017 0.001 PHE O 81 TYR 0.015 0.001 TYR N 81 ARG 0.020 0.000 ARG J 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17415.78 seconds wall clock time: 307 minutes 58.54 seconds (18478.54 seconds total)