Starting phenix.real_space_refine on Sat Jan 20 02:13:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq6_30437/01_2024/7cq6_30437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq6_30437/01_2024/7cq6_30437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq6_30437/01_2024/7cq6_30437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq6_30437/01_2024/7cq6_30437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq6_30437/01_2024/7cq6_30437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq6_30437/01_2024/7cq6_30437.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 Cl 4 4.86 5 C 8674 2.51 5 N 2228 2.21 5 O 2396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 526": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 640": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ARG 775": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13392 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1648 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 199} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1642 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 4996 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 620} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5046 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.13, per 1000 atoms: 0.53 Number of scatterers: 13392 At special positions: 0 Unit cell: (134.193, 113.464, 127.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 90 16.00 O 2396 8.00 N 2228 7.00 C 8674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.02 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.06 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.06 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.02 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.04 Simple disulfide: pdb=" SG CYS D 438 " - pdb=" SG CYS D 454 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN A 263 " " NAG F 1 " - " ASN B 263 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 2.5 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 8 sheets defined 63.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 83 through 105 removed outlier: 3.858A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 88 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.547A pdb=" N GLN A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.795A pdb=" N CYS A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'A' and resid 224 through 244 removed outlier: 3.685A pdb=" N TYR A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Processing helix chain 'A' and resid 282 through 306 removed outlier: 3.524A pdb=" N PHE A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'B' and resid 90 through 105 removed outlier: 3.518A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.693A pdb=" N CYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 131 removed outlier: 3.780A pdb=" N ASP B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.695A pdb=" N SER B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 removed outlier: 3.548A pdb=" N ASN B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 244 removed outlier: 3.604A pdb=" N TYR B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.854A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.827A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.801A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 115 removed outlier: 3.585A pdb=" N ARG C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 170 removed outlier: 4.708A pdb=" N ARG C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.975A pdb=" N VAL C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.618A pdb=" N ALA C 202 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 223 through 240 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.744A pdb=" N SER C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.754A pdb=" N ARG C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 302 removed outlier: 4.018A pdb=" N ARG C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 314 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 374 through 405 removed outlier: 3.692A pdb=" N PHE C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 380 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 434 removed outlier: 3.527A pdb=" N ALA C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 428 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 486 through 503 removed outlier: 3.955A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 536 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.812A pdb=" N TYR C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 Processing helix chain 'C' and resid 579 through 595 Processing helix chain 'C' and resid 600 through 609 removed outlier: 4.029A pdb=" N GLN C 609 " --> pdb=" O HIS C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 630 removed outlier: 3.551A pdb=" N GLU C 629 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 681 through 688 Processing helix chain 'C' and resid 753 through 764 removed outlier: 3.567A pdb=" N LEU C 760 " --> pdb=" O ARG C 756 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 789 removed outlier: 3.665A pdb=" N ALA C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 121 through 170 removed outlier: 3.504A pdb=" N TRP D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLU D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.510A pdb=" N LEU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.659A pdb=" N ALA D 202 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 removed outlier: 3.641A pdb=" N ASN D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 240 removed outlier: 3.509A pdb=" N LEU D 227 " --> pdb=" O ARG D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 264 removed outlier: 4.215A pdb=" N GLN D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 removed outlier: 3.628A pdb=" N ARG D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP D 287 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 Processing helix chain 'D' and resid 320 through 346 removed outlier: 3.594A pdb=" N HIS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 407 removed outlier: 3.709A pdb=" N PHE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D 405 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 434 removed outlier: 3.816A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 486 through 505 removed outlier: 3.516A pdb=" N LEU D 495 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 536 removed outlier: 3.568A pdb=" N SER D 517 " --> pdb=" O VAL D 513 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 560 removed outlier: 3.567A pdb=" N TYR D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 3.804A pdb=" N VAL D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 596 Processing helix chain 'D' and resid 600 through 608 Processing helix chain 'D' and resid 646 through 651 Processing helix chain 'D' and resid 681 through 688 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 784 through 788 Processing sheet with id=AA1, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 439 Processing sheet with id=AA3, first strand: chain 'C' and resid 638 through 639 removed outlier: 6.614A pdb=" N LEU C 638 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 747 through 749 removed outlier: 6.711A pdb=" N VAL C 748 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 780 " --> pdb=" O VAL C 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 438 through 439 Processing sheet with id=AA6, first strand: chain 'D' and resid 638 through 639 removed outlier: 5.502A pdb=" N LEU D 638 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 641 through 643 Processing sheet with id=AA8, first strand: chain 'D' and resid 747 through 749 removed outlier: 4.431A pdb=" N GLY D 780 " --> pdb=" O VAL D 771 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2190 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: 4.03 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3823 1.33 - 1.46: 2746 1.46 - 1.58: 6973 1.58 - 1.70: 0 1.70 - 1.82: 137 Bond restraints: 13679 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CB PRO C 582 " pdb=" CG PRO C 582 " ideal model delta sigma weight residual 1.492 1.381 0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CG1 ILE D 229 " pdb=" CD1 ILE D 229 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.48e+00 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 13674 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.80: 250 104.80 - 112.22: 6598 112.22 - 119.64: 5155 119.64 - 127.06: 6400 127.06 - 134.47: 166 Bond angle restraints: 18569 Sorted by residual: angle pdb=" C GLY D 205 " pdb=" N ILE D 206 " pdb=" CA ILE D 206 " ideal model delta sigma weight residual 120.24 124.67 -4.43 6.30e-01 2.52e+00 4.94e+01 angle pdb=" N ILE D 114 " pdb=" CA ILE D 114 " pdb=" C ILE D 114 " ideal model delta sigma weight residual 113.53 107.51 6.02 9.80e-01 1.04e+00 3.77e+01 angle pdb=" N THR D 633 " pdb=" CA THR D 633 " pdb=" C THR D 633 " ideal model delta sigma weight residual 109.81 119.95 -10.14 2.21e+00 2.05e-01 2.10e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 ... (remaining 18564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 7716 15.81 - 31.62: 380 31.62 - 47.44: 54 47.44 - 63.25: 5 63.25 - 79.06: 6 Dihedral angle restraints: 8161 sinusoidal: 3208 harmonic: 4953 Sorted by residual: dihedral pdb=" CA CYS B 115 " pdb=" C CYS B 115 " pdb=" N TYR B 116 " pdb=" CA TYR B 116 " ideal model delta harmonic sigma weight residual 180.00 144.48 35.52 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CA ILE D 218 " pdb=" C ILE D 218 " pdb=" N PRO D 219 " pdb=" CA PRO D 219 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PRO A 108 " pdb=" C PRO A 108 " pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1521 0.061 - 0.122: 538 0.122 - 0.183: 100 0.183 - 0.244: 18 0.244 - 0.305: 2 Chirality restraints: 2179 Sorted by residual: chirality pdb=" CB VAL C 513 " pdb=" CA VAL C 513 " pdb=" CG1 VAL C 513 " pdb=" CG2 VAL C 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ARG B 107 " pdb=" N ARG B 107 " pdb=" C ARG B 107 " pdb=" CB ARG B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG A 107 " pdb=" N ARG A 107 " pdb=" C ARG A 107 " pdb=" CB ARG A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2176 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.035 2.00e-02 2.50e+03 2.68e-02 1.79e+01 pdb=" CG TRP C 179 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 179 " 0.034 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" CG TRP D 179 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP D 179 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 179 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 179 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 179 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 179 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 272 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C THR B 272 " 0.054 2.00e-02 2.50e+03 pdb=" O THR B 272 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE B 273 " -0.018 2.00e-02 2.50e+03 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2604 2.77 - 3.30: 12417 3.30 - 3.83: 21284 3.83 - 4.37: 25495 4.37 - 4.90: 44859 Nonbonded interactions: 106659 Sorted by model distance: nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.233 2.440 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.270 2.440 nonbonded pdb=" O LEU D 500 " pdb=" OG1 THR D 504 " model vdw 2.274 2.440 nonbonded pdb=" OG SER D 298 " pdb=" OG1 THR D 335 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASP A 76 " pdb=" OG SER A 145 " model vdw 2.301 2.440 ... (remaining 106654 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 73 through 245 or resid 253 through 306)) selection = (chain 'B' and (resid 73 through 204 or resid 216 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 617 or resid 625 through 652 or resid 657 throu \ gh 688 or resid 708 through 790 or resid 901 through 902)) selection = (chain 'D' and (resid 94 through 366 or (resid 367 and (name N or name CA or nam \ e C or name O or name CB )) or resid 368 through 617 or resid 625 through 688 or \ (resid 708 through 710 and (name N or name CA or name C or name O or name CB )) \ or resid 711 through 716 or resid 736 through 790 or resid 901 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.310 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: 0.010 Extract box with map and model: 5.520 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 36.370 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.010 0.111 13679 Z= 0.666 Angle : 1.121 10.136 18569 Z= 0.604 Chirality : 0.062 0.305 2179 Planarity : 0.008 0.067 2324 Dihedral : 9.887 79.060 4920 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.27 % Allowed : 2.06 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.15), residues: 1672 helix: -2.65 (0.11), residues: 1051 sheet: -3.33 (1.71), residues: 5 loop : -3.32 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.006 TRP D 179 HIS 0.010 0.002 HIS C 479 PHE 0.031 0.004 PHE C 329 TYR 0.029 0.003 TYR C 406 ARG 0.020 0.002 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 234 time to evaluate : 1.652 Fit side-chains REVERT: A 160 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 244 LEU cc_start: 0.7406 (pp) cc_final: 0.7206 (pp) REVERT: B 229 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8152 (mtmt) REVERT: B 238 MET cc_start: 0.7698 (mtt) cc_final: 0.7485 (mtm) REVERT: B 286 ILE cc_start: 0.8480 (mm) cc_final: 0.8159 (mt) REVERT: C 111 GLU cc_start: 0.6681 (tt0) cc_final: 0.6045 (mt-10) REVERT: C 287 ASP cc_start: 0.8207 (m-30) cc_final: 0.7889 (m-30) REVERT: C 562 MET cc_start: 0.8087 (ptp) cc_final: 0.7754 (ptm) REVERT: C 648 VAL cc_start: 0.7876 (t) cc_final: 0.7648 (p) REVERT: C 674 ARG cc_start: 0.7046 (mtm-85) cc_final: 0.6572 (ttm110) REVERT: D 107 PHE cc_start: 0.7666 (t80) cc_final: 0.7385 (t80) REVERT: D 217 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7731 (mtpt) REVERT: D 274 LYS cc_start: 0.5830 (mttt) cc_final: 0.5611 (pttt) REVERT: D 584 MET cc_start: 0.8682 (ptm) cc_final: 0.8299 (ttp) REVERT: D 658 HIS cc_start: 0.6323 (m-70) cc_final: 0.6106 (m-70) REVERT: D 759 LYS cc_start: 0.7535 (ttpt) cc_final: 0.7040 (ttpt) REVERT: D 760 LEU cc_start: 0.7549 (mt) cc_final: 0.7345 (mm) outliers start: 4 outliers final: 1 residues processed: 237 average time/residue: 1.6081 time to fit residues: 408.6650 Evaluate side-chains 167 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 479 HIS C 555 GLN C 657 ASN C 777 GLN D 162 ASN D 220 HIS D 263 GLN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN D 657 ASN D 683 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13679 Z= 0.191 Angle : 0.628 12.227 18569 Z= 0.327 Chirality : 0.040 0.160 2179 Planarity : 0.005 0.050 2324 Dihedral : 5.637 42.189 1916 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.99 % Allowed : 7.35 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 1672 helix: -0.33 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -3.04 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 179 HIS 0.004 0.001 HIS C 605 PHE 0.017 0.001 PHE D 392 TYR 0.014 0.001 TYR B 188 ARG 0.004 0.001 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.491 Fit side-chains REVERT: A 144 ARG cc_start: 0.7550 (pmt-80) cc_final: 0.7178 (pmm150) REVERT: A 160 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 195 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7432 (t-90) REVERT: A 237 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 281 ASP cc_start: 0.7730 (t0) cc_final: 0.7458 (t0) REVERT: B 167 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: B 168 GLU cc_start: 0.7602 (tp30) cc_final: 0.7057 (tp30) REVERT: B 229 LYS cc_start: 0.8461 (mmpt) cc_final: 0.8160 (mtmt) REVERT: C 99 TYR cc_start: 0.8091 (t80) cc_final: 0.7729 (t80) REVERT: C 111 GLU cc_start: 0.6662 (tt0) cc_final: 0.6042 (mt-10) REVERT: C 648 VAL cc_start: 0.7717 (t) cc_final: 0.7440 (p) REVERT: D 107 PHE cc_start: 0.7520 (t80) cc_final: 0.7218 (t80) REVERT: D 217 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7852 (mtpt) REVERT: D 566 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8992 (tt) REVERT: D 584 MET cc_start: 0.8528 (ptm) cc_final: 0.8289 (ttp) REVERT: D 617 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6022 (mm-30) REVERT: D 730 GLU cc_start: 0.5975 (mt-10) cc_final: 0.5672 (mt-10) REVERT: D 731 ARG cc_start: 0.5288 (mtt90) cc_final: 0.5086 (mmp-170) REVERT: D 759 LYS cc_start: 0.7201 (ttpt) cc_final: 0.6617 (ttpt) outliers start: 29 outliers final: 8 residues processed: 197 average time/residue: 1.4089 time to fit residues: 301.5063 Evaluate side-chains 175 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 754 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 439 GLN ** C 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13679 Z= 0.345 Angle : 0.679 13.767 18569 Z= 0.348 Chirality : 0.044 0.178 2179 Planarity : 0.005 0.051 2324 Dihedral : 5.333 34.615 1915 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.47 % Allowed : 9.62 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1672 helix: 0.41 (0.16), residues: 1064 sheet: -2.71 (2.01), residues: 5 loop : -2.89 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 179 HIS 0.008 0.001 HIS C 479 PHE 0.019 0.002 PHE C 392 TYR 0.014 0.002 TYR B 188 ARG 0.007 0.001 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.636 Fit side-chains REVERT: A 160 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 195 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7501 (t-90) REVERT: B 229 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8116 (mtpt) REVERT: C 111 GLU cc_start: 0.6479 (tt0) cc_final: 0.5818 (mt-10) REVERT: C 599 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: C 648 VAL cc_start: 0.7603 (t) cc_final: 0.7354 (p) REVERT: C 676 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.5099 (mp10) REVERT: D 107 PHE cc_start: 0.7588 (t80) cc_final: 0.7328 (t80) REVERT: D 217 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7864 (mtpt) REVERT: D 584 MET cc_start: 0.8524 (ptm) cc_final: 0.8321 (ttp) REVERT: D 617 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.5890 (mm-30) REVERT: D 730 GLU cc_start: 0.5939 (mt-10) cc_final: 0.5687 (mt-10) REVERT: D 731 ARG cc_start: 0.5371 (mtt90) cc_final: 0.5084 (mmp-170) REVERT: D 759 LYS cc_start: 0.7337 (ttpt) cc_final: 0.6789 (ttmt) outliers start: 36 outliers final: 14 residues processed: 187 average time/residue: 1.3973 time to fit residues: 284.4430 Evaluate side-chains 174 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 757 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 623 HIS ** C 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13679 Z= 0.168 Angle : 0.566 11.066 18569 Z= 0.291 Chirality : 0.040 0.152 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.671 25.920 1915 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1672 helix: 1.09 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 524 HIS 0.005 0.001 HIS C 605 PHE 0.012 0.001 PHE D 392 TYR 0.014 0.001 TYR B 116 ARG 0.005 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.679 Fit side-chains REVERT: A 144 ARG cc_start: 0.7516 (pmt-80) cc_final: 0.7101 (pmm150) REVERT: A 160 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 195 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7437 (t-90) REVERT: A 237 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 281 ASP cc_start: 0.7676 (t0) cc_final: 0.7456 (t0) REVERT: B 167 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.6881 (mp10) REVERT: B 229 LYS cc_start: 0.8533 (mmpt) cc_final: 0.8261 (mtmt) REVERT: C 99 TYR cc_start: 0.7909 (t80) cc_final: 0.7499 (t80) REVERT: C 111 GLU cc_start: 0.6557 (tt0) cc_final: 0.5855 (mt-10) REVERT: C 648 VAL cc_start: 0.7570 (t) cc_final: 0.7351 (p) REVERT: D 107 PHE cc_start: 0.7450 (t80) cc_final: 0.7147 (t80) REVERT: D 217 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7878 (mtpt) REVERT: D 566 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8996 (tt) REVERT: D 617 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.5955 (mm-30) REVERT: D 759 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6677 (ttmt) outliers start: 31 outliers final: 9 residues processed: 185 average time/residue: 1.4005 time to fit residues: 281.6288 Evaluate side-chains 163 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN C 439 GLN C 768 HIS ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13679 Z= 0.212 Angle : 0.577 11.845 18569 Z= 0.296 Chirality : 0.040 0.146 2179 Planarity : 0.004 0.047 2324 Dihedral : 4.563 28.847 1915 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.06 % Allowed : 12.09 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1672 helix: 1.35 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : -2.63 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 524 HIS 0.005 0.001 HIS C 605 PHE 0.015 0.001 PHE D 392 TYR 0.014 0.001 TYR A 116 ARG 0.004 0.000 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 195 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7444 (t-90) REVERT: A 242 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7634 (t0) REVERT: B 229 LYS cc_start: 0.8499 (mmpt) cc_final: 0.8182 (mtmt) REVERT: C 99 TYR cc_start: 0.7950 (t80) cc_final: 0.7517 (t80) REVERT: C 111 GLU cc_start: 0.6589 (tt0) cc_final: 0.5831 (mt-10) REVERT: C 599 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: C 648 VAL cc_start: 0.7560 (t) cc_final: 0.7341 (p) REVERT: D 107 PHE cc_start: 0.7460 (t80) cc_final: 0.7236 (t80) REVERT: D 217 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7883 (mtpt) REVERT: D 566 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9029 (tt) REVERT: D 584 MET cc_start: 0.8412 (ttp) cc_final: 0.8118 (ttm) REVERT: D 617 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.5921 (mm-30) REVERT: D 731 ARG cc_start: 0.5706 (OUTLIER) cc_final: 0.5107 (mmp-170) REVERT: D 759 LYS cc_start: 0.7439 (ttpt) cc_final: 0.6884 (ttmt) outliers start: 30 outliers final: 12 residues processed: 171 average time/residue: 1.3971 time to fit residues: 260.8718 Evaluate side-chains 161 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 731 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 0.0770 chunk 40 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 242 ASN C 439 GLN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13679 Z= 0.198 Angle : 0.571 11.553 18569 Z= 0.293 Chirality : 0.040 0.142 2179 Planarity : 0.004 0.049 2324 Dihedral : 4.466 26.911 1915 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.27 % Allowed : 12.57 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1672 helix: 1.54 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 524 HIS 0.009 0.001 HIS D 373 PHE 0.014 0.001 PHE D 392 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7481 (t-90) REVERT: B 152 MET cc_start: 0.7672 (ttm) cc_final: 0.7464 (ttt) REVERT: B 229 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8152 (mtmt) REVERT: C 99 TYR cc_start: 0.7956 (t80) cc_final: 0.7522 (t80) REVERT: C 111 GLU cc_start: 0.6591 (tt0) cc_final: 0.5846 (mt-10) REVERT: C 599 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: C 648 VAL cc_start: 0.7552 (t) cc_final: 0.7339 (p) REVERT: C 741 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.6690 (pmm) REVERT: D 107 PHE cc_start: 0.7448 (t80) cc_final: 0.7221 (t80) REVERT: D 566 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9023 (tt) REVERT: D 617 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.5917 (mm-30) REVERT: D 731 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5158 (mmp-170) REVERT: D 759 LYS cc_start: 0.7460 (ttpt) cc_final: 0.6903 (ttmt) REVERT: D 785 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7161 (mptt) outliers start: 33 outliers final: 16 residues processed: 168 average time/residue: 1.2752 time to fit residues: 233.7390 Evaluate side-chains 164 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 731 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 137 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 242 ASN C 439 GLN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 13679 Z= 0.155 Angle : 0.543 10.511 18569 Z= 0.278 Chirality : 0.039 0.136 2179 Planarity : 0.004 0.048 2324 Dihedral : 4.304 25.845 1915 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.40 % Allowed : 12.98 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1672 helix: 1.80 (0.16), residues: 1066 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 524 HIS 0.006 0.001 HIS D 373 PHE 0.012 0.001 PHE D 392 TYR 0.013 0.001 TYR A 116 ARG 0.003 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.564 Fit side-chains REVERT: A 144 ARG cc_start: 0.7409 (pmt-80) cc_final: 0.7082 (pmm150) REVERT: A 195 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7413 (t-90) REVERT: B 152 MET cc_start: 0.7647 (ttm) cc_final: 0.7444 (ttt) REVERT: B 229 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8128 (mtmt) REVERT: C 111 GLU cc_start: 0.6589 (tt0) cc_final: 0.5852 (mt-10) REVERT: C 628 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5506 (tmm-80) REVERT: C 741 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.6635 (pmm) REVERT: D 97 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6131 (pp) REVERT: D 107 PHE cc_start: 0.7408 (t80) cc_final: 0.7106 (t80) REVERT: D 566 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8998 (tt) REVERT: D 584 MET cc_start: 0.8362 (ttp) cc_final: 0.8116 (ptm) REVERT: D 617 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.5899 (mm-30) REVERT: D 731 ARG cc_start: 0.5864 (ptm-80) cc_final: 0.5147 (mmp-170) REVERT: D 759 LYS cc_start: 0.7460 (ttpt) cc_final: 0.6891 (ttmt) REVERT: D 785 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7131 (mptt) outliers start: 35 outliers final: 13 residues processed: 179 average time/residue: 1.1389 time to fit residues: 223.6851 Evaluate side-chains 169 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13679 Z= 0.209 Angle : 0.571 10.939 18569 Z= 0.291 Chirality : 0.041 0.166 2179 Planarity : 0.004 0.048 2324 Dihedral : 4.353 26.346 1915 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.61 % Allowed : 13.46 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1672 helix: 1.82 (0.16), residues: 1066 sheet: None (None), residues: 0 loop : -2.53 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 524 HIS 0.005 0.001 HIS C 605 PHE 0.015 0.001 PHE D 392 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7540 (t-90) REVERT: B 110 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7552 (mpt180) REVERT: B 229 LYS cc_start: 0.8452 (mmpt) cc_final: 0.8142 (mtmt) REVERT: C 111 GLU cc_start: 0.6667 (tt0) cc_final: 0.5941 (mt-10) REVERT: C 628 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5638 (tmm-80) REVERT: C 741 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.6619 (pmm) REVERT: D 97 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6156 (pp) REVERT: D 107 PHE cc_start: 0.7431 (t80) cc_final: 0.7221 (t80) REVERT: D 566 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9027 (tt) REVERT: D 617 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6067 (mm-30) REVERT: D 731 ARG cc_start: 0.5887 (ptm-80) cc_final: 0.5163 (mmp-170) REVERT: D 759 LYS cc_start: 0.7485 (ttpt) cc_final: 0.6941 (ttmt) REVERT: D 785 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7116 (mptt) outliers start: 38 outliers final: 18 residues processed: 171 average time/residue: 1.3027 time to fit residues: 243.2940 Evaluate side-chains 170 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 733 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13679 Z= 0.204 Angle : 0.568 11.208 18569 Z= 0.291 Chirality : 0.040 0.155 2179 Planarity : 0.004 0.048 2324 Dihedral : 4.339 26.810 1915 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.61 % Allowed : 13.87 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1672 helix: 1.94 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 PHE 0.015 0.001 PHE D 392 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 1.426 Fit side-chains REVERT: A 144 ARG cc_start: 0.7464 (pmt-80) cc_final: 0.7083 (pmm150) REVERT: A 195 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7555 (t-90) REVERT: B 110 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7589 (mpt180) REVERT: B 229 LYS cc_start: 0.8441 (mmpt) cc_final: 0.8168 (mtmt) REVERT: C 111 GLU cc_start: 0.6671 (tt0) cc_final: 0.5930 (mt-10) REVERT: C 628 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.5697 (tmm-80) REVERT: C 639 ARG cc_start: 0.7061 (ttp80) cc_final: 0.6429 (mtm180) REVERT: C 741 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.6596 (pmm) REVERT: D 97 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6047 (pp) REVERT: D 566 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9027 (tt) REVERT: D 617 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6077 (mm-30) REVERT: D 731 ARG cc_start: 0.5750 (ptm-80) cc_final: 0.5056 (mmp-170) REVERT: D 759 LYS cc_start: 0.7551 (ttpt) cc_final: 0.6974 (ttmt) REVERT: D 785 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7129 (mptt) outliers start: 38 outliers final: 17 residues processed: 167 average time/residue: 1.2679 time to fit residues: 231.2014 Evaluate side-chains 172 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 733 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 13 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 242 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13679 Z= 0.161 Angle : 0.547 9.527 18569 Z= 0.279 Chirality : 0.039 0.161 2179 Planarity : 0.004 0.048 2324 Dihedral : 4.170 24.567 1915 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.79 % Allowed : 14.77 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1672 helix: 2.17 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 PHE 0.012 0.001 PHE C 392 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG D 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7379 (pmt-80) cc_final: 0.7047 (pmm150) REVERT: A 160 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7322 (mt-10) REVERT: B 168 GLU cc_start: 0.7527 (tp30) cc_final: 0.6937 (tp30) REVERT: B 229 LYS cc_start: 0.8454 (mmpt) cc_final: 0.8158 (mtmt) REVERT: C 111 GLU cc_start: 0.6669 (tt0) cc_final: 0.5943 (mt-10) REVERT: C 628 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5584 (tmm-80) REVERT: C 639 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6410 (mtm180) REVERT: D 97 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6040 (pp) REVERT: D 107 PHE cc_start: 0.7413 (t80) cc_final: 0.7190 (t80) REVERT: D 566 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9049 (tt) REVERT: D 731 ARG cc_start: 0.5791 (ptm-80) cc_final: 0.5075 (mmp-170) REVERT: D 759 LYS cc_start: 0.7465 (ttpt) cc_final: 0.6846 (ttpt) REVERT: D 785 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7092 (mptt) outliers start: 26 outliers final: 13 residues processed: 178 average time/residue: 1.2884 time to fit residues: 250.7072 Evaluate side-chains 166 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 733 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 242 ASN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107883 restraints weight = 17143.847| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.69 r_work: 0.3071 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13679 Z= 0.180 Angle : 0.557 9.744 18569 Z= 0.286 Chirality : 0.040 0.158 2179 Planarity : 0.004 0.047 2324 Dihedral : 4.171 25.652 1915 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.99 % Allowed : 15.11 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1672 helix: 2.17 (0.16), residues: 1057 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 PHE 0.013 0.001 PHE D 392 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG D 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4874.69 seconds wall clock time: 93 minutes 35.97 seconds (5615.97 seconds total)