Starting phenix.real_space_refine on Wed Feb 21 19:49:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8y_24249/02_2024/7n8y_24249.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8y_24249/02_2024/7n8y_24249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8y_24249/02_2024/7n8y_24249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8y_24249/02_2024/7n8y_24249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8y_24249/02_2024/7n8y_24249.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8y_24249/02_2024/7n8y_24249.pdb" } resolution = 3.65 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15708 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10199 2.51 5 N 2852 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 93": "OD1" <-> "OD2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 616": "OD1" <-> "OD2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B ARG 658": "NH1" <-> "NH2" Residue "B ARG 678": "NH1" <-> "NH2" Residue "B ASP 691": "OD1" <-> "OD2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B ASP 722": "OD1" <-> "OD2" Residue "B ASP 764": "OD1" <-> "OD2" Residue "B GLU 771": "OE1" <-> "OE2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D ASP 423": "OD1" <-> "OD2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 571": "OE1" <-> "OE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 579": "OD1" <-> "OD2" Residue "D ASP 589": "OD1" <-> "OD2" Residue "D TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 620": "OD1" <-> "OD2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D ARG 658": "NH1" <-> "NH2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D GLU 699": "OE1" <-> "OE2" Residue "D ASP 722": "OD1" <-> "OD2" Residue "D TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 764": "OD1" <-> "OD2" Residue "D GLU 770": "OE1" <-> "OE2" Residue "D GLU 771": "OE1" <-> "OE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "D PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16162 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1964 Classifications: {'peptide': 242} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 227} Chain: "B" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6116 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 759} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1964 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 227} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6118 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 759} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 10.93, per 1000 atoms: 0.68 Number of scatterers: 16162 At special positions: 0 Unit cell: (169.52, 142.48, 120.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3039 8.00 N 2852 7.00 C 10199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.9 seconds 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3820 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 32 sheets defined 25.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.014A pdb=" N THR A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 235 removed outlier: 4.364A pdb=" N THR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.705A pdb=" N ASN A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.566A pdb=" N PHE A 316 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 231 through 241 removed outlier: 4.183A pdb=" N LYS B 237 " --> pdb=" O TRP B 233 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 removed outlier: 4.146A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 4.059A pdb=" N HIS B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 4.161A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 382 removed outlier: 4.829A pdb=" N GLU B 374 " --> pdb=" O TYR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.837A pdb=" N ASP B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 4.329A pdb=" N GLU B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.866A pdb=" N VAL B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.979A pdb=" N VAL B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 626 removed outlier: 3.765A pdb=" N ALA B 623 " --> pdb=" O GLY B 619 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.515A pdb=" N ARG B 671 " --> pdb=" O GLU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 689 No H-bonds generated for 'chain 'B' and resid 687 through 689' Processing helix chain 'B' and resid 770 through 784 removed outlier: 3.604A pdb=" N ILE B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA B 775 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 776 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 789 removed outlier: 3.668A pdb=" N PHE B 789 " --> pdb=" O LYS B 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.015A pdb=" N THR C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 235 removed outlier: 4.365A pdb=" N THR C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.706A pdb=" N ASN C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.566A pdb=" N PHE C 316 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'D' and resid 4 through 12 removed outlier: 4.169A pdb=" N LEU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 4.072A pdb=" N ALA D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 29 removed outlier: 4.112A pdb=" N GLY D 29 " --> pdb=" O THR D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 26 through 29' Processing helix chain 'D' and resid 146 through 151 Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.831A pdb=" N CYS D 169 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D 170 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY D 171 " --> pdb=" O ASP D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 171' Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 231 through 240 removed outlier: 4.271A pdb=" N LYS D 237 " --> pdb=" O TRP D 233 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.763A pdb=" N VAL D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 369 through 384 removed outlier: 4.111A pdb=" N ARG D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 418 Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.765A pdb=" N ASP D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 4.271A pdb=" N GLU D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 503 removed outlier: 4.048A pdb=" N VAL D 498 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 525 removed outlier: 3.729A pdb=" N GLN D 522 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 524 " --> pdb=" O VAL D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 560 removed outlier: 4.391A pdb=" N ALA D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 613 through 626 removed outlier: 3.924A pdb=" N LEU D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 623 " --> pdb=" O GLY D 619 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 689 No H-bonds generated for 'chain 'D' and resid 687 through 689' Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 770 through 786 removed outlier: 3.765A pdb=" N ALA D 784 " --> pdb=" O LYS D 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 removed outlier: 6.213A pdb=" N THR A 126 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 193 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 206 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 295 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY A 292 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.405A pdb=" N THR B 157 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL B 35 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 159 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 31 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AA5, first strand: chain 'B' and resid 205 through 207 removed outlier: 3.621A pdb=" N ARG B 279 " --> pdb=" O VAL B 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 216 removed outlier: 3.529A pdb=" N VAL B 394 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 267 through 268 removed outlier: 3.648A pdb=" N ASP B 387 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 405 through 409 removed outlier: 3.642A pdb=" N ALA B 446 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 447 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 436 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 509 removed outlier: 6.531A pdb=" N GLN B 508 " --> pdb=" O PHE B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 515 through 516 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 574 Processing sheet with id=AB4, first strand: chain 'B' and resid 572 through 574 removed outlier: 3.575A pdb=" N VAL B 681 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N GLY B 660 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 10.289A pdb=" N SER B 649 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N ILE B 662 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N GLY B 647 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 664 " --> pdb=" O HIS B 645 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 577 through 578 Processing sheet with id=AB6, first strand: chain 'B' and resid 636 through 637 removed outlier: 3.759A pdb=" N LYS B 637 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.099A pdb=" N VAL B 736 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 761 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 738 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 759 " --> pdb=" O VAL B 738 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.099A pdb=" N VAL B 736 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 761 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 738 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 759 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 712 " --> pdb=" O LEU B 756 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 706 " --> pdb=" O LEU B 762 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 713 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 791 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.213A pdb=" N THR C 126 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 193 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 206 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 295 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY C 292 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AC2, first strand: chain 'D' and resid 2 through 3 removed outlier: 6.273A pdb=" N THR D 157 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D 35 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU D 159 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 161 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU D 31 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 43 through 47 removed outlier: 7.308A pdb=" N GLY D 44 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 94 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'D' and resid 205 through 207 removed outlier: 7.201A pdb=" N THR D 206 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N MET D 280 " --> pdb=" O THR D 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 279 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 215 through 216 Processing sheet with id=AC7, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AC8, first strand: chain 'D' and resid 286 through 288 Processing sheet with id=AC9, first strand: chain 'D' and resid 405 through 409 removed outlier: 3.670A pdb=" N ALA D 446 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 436 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 508 through 509 removed outlier: 6.181A pdb=" N GLN D 508 " --> pdb=" O PHE D 570 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR D 572 " --> pdb=" O GLN D 508 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 571 " --> pdb=" O ALA D 593 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE D 682 " --> pdb=" O GLY D 594 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 681 " --> pdb=" O GLY D 663 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 660 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 652 " --> pdb=" O GLY D 660 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 662 " --> pdb=" O ALA D 650 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN D 648 " --> pdb=" O VAL D 664 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 637 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 515 through 516 removed outlier: 4.588A pdb=" N LEU D 531 " --> pdb=" O MET D 544 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 577 through 578 Processing sheet with id=AD4, first strand: chain 'D' and resid 706 through 708 removed outlier: 3.670A pdb=" N GLY D 737 " --> pdb=" O ILE D 761 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 711 through 714 removed outlier: 3.786A pdb=" N VAL D 714 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 754 " --> pdb=" O VAL D 714 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 5.76 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: 5100 1.33 - 1.45: 2377 1.45 - 1.57: 8875 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 16468 Sorted by residual: bond pdb=" N ILE C 185 " pdb=" CA ILE C 185 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.14e-02 7.69e+03 1.26e+01 bond pdb=" N ILE A 185 " pdb=" CA ILE A 185 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.15e-02 7.56e+03 1.12e+01 bond pdb=" N LEU B 673 " pdb=" CA LEU B 673 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.81e+00 bond pdb=" N GLN C 181 " pdb=" CA GLN C 181 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.98e+00 bond pdb=" CA THR B 628 " pdb=" C THR B 628 " ideal model delta sigma weight residual 1.523 1.561 -0.039 1.41e-02 5.03e+03 7.53e+00 ... (remaining 16463 not shown) Histogram of bond angle deviations from ideal: 96.84 - 105.15: 343 105.15 - 113.46: 9130 113.46 - 121.76: 8865 121.76 - 130.07: 3905 130.07 - 138.38: 96 Bond angle restraints: 22339 Sorted by residual: angle pdb=" N LYS B 688 " pdb=" CA LYS B 688 " pdb=" C LYS B 688 " ideal model delta sigma weight residual 114.56 107.65 6.91 1.27e+00 6.20e-01 2.96e+01 angle pdb=" N PRO C 183 " pdb=" CA PRO C 183 " pdb=" C PRO C 183 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.95e+01 angle pdb=" N PRO C 183 " pdb=" CA PRO C 183 " pdb=" CB PRO C 183 " ideal model delta sigma weight residual 103.08 98.08 5.00 9.70e-01 1.06e+00 2.66e+01 angle pdb=" N PRO C 184 " pdb=" CA PRO C 184 " pdb=" CB PRO C 184 " ideal model delta sigma weight residual 103.25 97.86 5.39 1.05e+00 9.07e-01 2.64e+01 angle pdb=" C ILE A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 127.00 138.38 -11.38 2.40e+00 1.74e-01 2.25e+01 ... (remaining 22334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.87: 9410 25.87 - 51.73: 506 51.73 - 77.60: 34 77.60 - 103.47: 6 103.47 - 129.33: 1 Dihedral angle restraints: 9957 sinusoidal: 4023 harmonic: 5934 Sorted by residual: dihedral pdb=" CA GLN C 182 " pdb=" C GLN C 182 " pdb=" N PRO C 183 " pdb=" CA PRO C 183 " ideal model delta harmonic sigma weight residual -180.00 -50.67 -129.33 0 5.00e+00 4.00e-02 6.69e+02 dihedral pdb=" CA THR D 196 " pdb=" C THR D 196 " pdb=" N ALA D 197 " pdb=" CA ALA D 197 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA VAL C 257 " pdb=" C VAL C 257 " pdb=" N ASP C 258 " pdb=" CA ASP C 258 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 9954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1754 0.052 - 0.104: 596 0.104 - 0.155: 132 0.155 - 0.207: 39 0.207 - 0.259: 11 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CB ILE B 634 " pdb=" CA ILE B 634 " pdb=" CG1 ILE B 634 " pdb=" CG2 ILE B 634 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB VAL B 612 " pdb=" CA VAL B 612 " pdb=" CG1 VAL B 612 " pdb=" CG2 VAL B 612 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE A 213 " pdb=" CA ILE A 213 " pdb=" CG1 ILE A 213 " pdb=" CG2 ILE A 213 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2529 not shown) Planarity restraints: 2945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 163 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO D 164 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 195 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C VAL D 195 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL D 195 " 0.019 2.00e-02 2.50e+03 pdb=" N THR D 196 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 672 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C LYS B 672 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS B 672 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 673 " -0.015 2.00e-02 2.50e+03 ... (remaining 2942 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4570 2.81 - 3.34: 13426 3.34 - 3.86: 24840 3.86 - 4.38: 27103 4.38 - 4.90: 48210 Nonbonded interactions: 118149 Sorted by model distance: nonbonded pdb=" OE1 GLU A 132 " pdb=" OH TYR A 194 " model vdw 2.293 2.440 nonbonded pdb=" OE1 GLU C 132 " pdb=" OH TYR C 194 " model vdw 2.294 2.440 nonbonded pdb=" O ALA B 721 " pdb=" OG SER B 725 " model vdw 2.298 2.440 nonbonded pdb=" OD1 ASN B 325 " pdb=" OG1 THR B 328 " model vdw 2.304 2.440 nonbonded pdb=" O SER B 514 " pdb=" OG SER B 514 " model vdw 2.314 2.440 ... (remaining 118144 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 791 or (resid 792 through 795 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 673 or (resid 674 and (name N or name CA or name \ C or name O or name CB )) or resid 675 through 795)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 4.600 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 46.940 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.005 0.082 16468 Z= 0.354 Angle : 0.984 11.379 22339 Z= 0.562 Chirality : 0.057 0.259 2532 Planarity : 0.007 0.074 2945 Dihedral : 14.983 129.332 6137 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.86 % Favored : 90.85 % Rotamer: Outliers : 0.69 % Allowed : 10.24 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -5.05 (0.14), residues: 2066 helix: -3.32 (0.16), residues: 450 sheet: -4.10 (0.25), residues: 212 loop : -3.48 (0.13), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 605 HIS 0.006 0.001 HIS D 666 PHE 0.027 0.003 PHE C 293 TYR 0.019 0.002 TYR B 150 ARG 0.006 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7367 (ttp-110) REVERT: A 182 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: A 196 ASN cc_start: 0.7573 (t0) cc_final: 0.7358 (t0) REVERT: A 274 MET cc_start: 0.7648 (mmm) cc_final: 0.7145 (mmm) REVERT: B 2 LYS cc_start: 0.7806 (ptpt) cc_final: 0.7564 (ptmm) REVERT: B 659 ILE cc_start: 0.8663 (tp) cc_final: 0.8306 (tp) REVERT: B 691 ASP cc_start: 0.7740 (p0) cc_final: 0.7177 (p0) REVERT: C 176 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7512 (ttp-110) REVERT: C 181 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: C 274 MET cc_start: 0.7508 (mmm) cc_final: 0.7084 (mmm) REVERT: D 19 ASP cc_start: 0.7269 (t0) cc_final: 0.7012 (t0) REVERT: D 251 ASP cc_start: 0.7110 (p0) cc_final: 0.6880 (p0) REVERT: D 362 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7689 (ptp-110) REVERT: D 424 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7465 (tm-30) REVERT: D 544 MET cc_start: 0.7756 (mmp) cc_final: 0.7435 (mmm) outliers start: 12 outliers final: 3 residues processed: 284 average time/residue: 0.3251 time to fit residues: 129.9857 Evaluate side-chains 186 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 139 ASN A 202 HIS ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 156 ASN B 339 ASN B 420 HIS B 480 GLN B 581 GLN B 734 GLN B 766 ASN C 107 HIS C 139 ASN C 181 GLN C 202 HIS ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 86 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 358 HIS D 581 GLN D 588 GLN D 635 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16468 Z= 0.169 Angle : 0.608 10.760 22339 Z= 0.318 Chirality : 0.044 0.164 2532 Planarity : 0.005 0.055 2945 Dihedral : 6.370 86.124 2265 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.00 % Favored : 90.95 % Rotamer: Outliers : 2.37 % Allowed : 16.03 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -4.19 (0.15), residues: 2066 helix: -2.07 (0.21), residues: 464 sheet: -3.09 (0.25), residues: 282 loop : -3.15 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 444 HIS 0.003 0.001 HIS C 149 PHE 0.020 0.001 PHE C 293 TYR 0.014 0.001 TYR C 137 ARG 0.003 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7483 (ttm110) cc_final: 0.7263 (ttp-110) REVERT: A 182 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: A 196 ASN cc_start: 0.7591 (t0) cc_final: 0.7341 (t0) REVERT: B 2 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7450 (ptmm) REVERT: B 65 THR cc_start: 0.7131 (OUTLIER) cc_final: 0.6721 (p) REVERT: B 428 ASP cc_start: 0.7714 (t0) cc_final: 0.7453 (t0) REVERT: B 451 TRP cc_start: 0.8783 (p90) cc_final: 0.8327 (p90) REVERT: B 659 ILE cc_start: 0.8590 (tp) cc_final: 0.8289 (tp) REVERT: B 691 ASP cc_start: 0.7680 (p0) cc_final: 0.7057 (p0) REVERT: C 198 TYR cc_start: 0.7890 (t80) cc_final: 0.7684 (t80) REVERT: D 362 ARG cc_start: 0.7994 (ptp-170) cc_final: 0.7715 (ptp-110) REVERT: D 424 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7440 (tm-30) REVERT: D 674 ASP cc_start: 0.5415 (OUTLIER) cc_final: 0.5139 (m-30) outliers start: 41 outliers final: 22 residues processed: 235 average time/residue: 0.2703 time to fit residues: 95.4351 Evaluate side-chains 194 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 674 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 0.0670 chunk 58 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 766 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS D 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16468 Z= 0.350 Angle : 0.696 11.269 22339 Z= 0.360 Chirality : 0.047 0.192 2532 Planarity : 0.005 0.076 2945 Dihedral : 6.375 84.272 2263 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 3.65 % Allowed : 18.81 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.88 (0.16), residues: 2066 helix: -1.71 (0.22), residues: 468 sheet: -2.76 (0.27), residues: 282 loop : -3.03 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 266 HIS 0.006 0.001 HIS C 149 PHE 0.026 0.002 PHE A 230 TYR 0.023 0.002 TYR B 507 ARG 0.004 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 195 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8074 (t0) cc_final: 0.7676 (t0) REVERT: B 1 MET cc_start: 0.4464 (ttt) cc_final: 0.4194 (ttt) REVERT: B 2 LYS cc_start: 0.7784 (ptpt) cc_final: 0.7558 (ptmm) REVERT: B 65 THR cc_start: 0.7176 (OUTLIER) cc_final: 0.6780 (p) REVERT: B 455 MET cc_start: 0.7291 (ttm) cc_final: 0.6756 (ttp) REVERT: B 653 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6781 (m-10) REVERT: B 659 ILE cc_start: 0.8892 (tp) cc_final: 0.8477 (tp) REVERT: B 691 ASP cc_start: 0.7803 (p0) cc_final: 0.7185 (p0) REVERT: C 274 MET cc_start: 0.7557 (mmm) cc_final: 0.7350 (mmm) REVERT: D 19 ASP cc_start: 0.7312 (t0) cc_final: 0.7045 (t0) REVERT: D 451 TRP cc_start: 0.8887 (p90) cc_final: 0.8245 (p90) REVERT: D 674 ASP cc_start: 0.5857 (OUTLIER) cc_final: 0.5147 (m-30) outliers start: 63 outliers final: 36 residues processed: 247 average time/residue: 0.2768 time to fit residues: 102.5128 Evaluate side-chains 213 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 97 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 188 optimal weight: 0.4980 chunk 199 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 472 ASN B 766 ASN C 196 ASN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16468 Z= 0.164 Angle : 0.562 9.463 22339 Z= 0.293 Chirality : 0.043 0.170 2532 Planarity : 0.004 0.057 2945 Dihedral : 5.141 44.662 2257 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.30 % Allowed : 20.54 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.44 (0.17), residues: 2066 helix: -1.21 (0.23), residues: 478 sheet: -2.46 (0.28), residues: 276 loop : -2.82 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 318 HIS 0.003 0.001 HIS A 149 PHE 0.023 0.001 PHE A 230 TYR 0.009 0.001 TYR B 507 ARG 0.002 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 186 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6755 (p) REVERT: B 455 MET cc_start: 0.7176 (ttm) cc_final: 0.6577 (ttp) REVERT: B 653 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: B 659 ILE cc_start: 0.8848 (tp) cc_final: 0.8453 (tp) REVERT: B 691 ASP cc_start: 0.7739 (p0) cc_final: 0.7073 (p0) REVERT: D 19 ASP cc_start: 0.7170 (t0) cc_final: 0.6891 (t0) REVERT: D 290 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5654 (tt) REVERT: D 362 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7721 (ptp-110) REVERT: D 379 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7176 (tt) REVERT: D 565 ASN cc_start: 0.5683 (p0) cc_final: 0.5476 (t0) outliers start: 57 outliers final: 35 residues processed: 231 average time/residue: 0.2532 time to fit residues: 89.5077 Evaluate side-chains 209 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 662 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.0470 chunk 169 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN D 156 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16468 Z= 0.247 Angle : 0.598 9.866 22339 Z= 0.310 Chirality : 0.045 0.165 2532 Planarity : 0.004 0.047 2945 Dihedral : 5.168 41.073 2257 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 4.98 % Allowed : 20.31 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.33 (0.17), residues: 2066 helix: -1.15 (0.23), residues: 478 sheet: -2.36 (0.29), residues: 276 loop : -2.74 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 444 HIS 0.006 0.001 HIS C 107 PHE 0.027 0.002 PHE D 317 TYR 0.017 0.001 TYR B 507 ARG 0.004 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 180 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7372 (ttp-110) REVERT: B 65 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6906 (p) REVERT: B 118 MET cc_start: 0.3898 (ptt) cc_final: 0.3314 (mtt) REVERT: B 455 MET cc_start: 0.7191 (ttm) cc_final: 0.6647 (ttp) REVERT: B 653 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6617 (m-10) REVERT: B 659 ILE cc_start: 0.8908 (tp) cc_final: 0.8500 (tp) REVERT: B 691 ASP cc_start: 0.7798 (p0) cc_final: 0.7144 (p0) REVERT: D 19 ASP cc_start: 0.7150 (t0) cc_final: 0.6853 (t0) REVERT: D 379 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7152 (tt) REVERT: D 451 TRP cc_start: 0.8890 (p90) cc_final: 0.8285 (p90) REVERT: D 565 ASN cc_start: 0.5817 (p0) cc_final: 0.5513 (t0) REVERT: D 674 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.5403 (m-30) outliers start: 86 outliers final: 59 residues processed: 251 average time/residue: 0.2581 time to fit residues: 99.1644 Evaluate side-chains 233 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 170 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 581 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 613 ASP Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 104 optimal weight: 7.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 GLN ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16468 Z= 0.260 Angle : 0.617 12.767 22339 Z= 0.318 Chirality : 0.045 0.161 2532 Planarity : 0.004 0.047 2945 Dihedral : 5.212 39.648 2257 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 5.32 % Allowed : 20.49 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.20 (0.17), residues: 2066 helix: -1.01 (0.23), residues: 466 sheet: -2.14 (0.31), residues: 242 loop : -2.70 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 444 HIS 0.006 0.001 HIS C 107 PHE 0.023 0.002 PHE A 230 TYR 0.018 0.001 TYR B 507 ARG 0.005 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 185 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.7929 (t) REVERT: A 176 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7357 (ttp-110) REVERT: B 65 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6890 (p) REVERT: B 118 MET cc_start: 0.3579 (ptt) cc_final: 0.3116 (mtt) REVERT: B 455 MET cc_start: 0.7075 (ttm) cc_final: 0.6566 (ttp) REVERT: B 653 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6738 (m-10) REVERT: B 659 ILE cc_start: 0.8887 (tp) cc_final: 0.8508 (tp) REVERT: B 691 ASP cc_start: 0.7775 (p0) cc_final: 0.7153 (p0) REVERT: D 19 ASP cc_start: 0.7245 (t0) cc_final: 0.6995 (t0) REVERT: D 168 ASP cc_start: 0.8111 (p0) cc_final: 0.7910 (p0) REVERT: D 379 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7059 (tt) REVERT: D 444 TRP cc_start: 0.8158 (m-90) cc_final: 0.7902 (m-90) REVERT: D 451 TRP cc_start: 0.8928 (p90) cc_final: 0.8323 (p90) REVERT: D 565 ASN cc_start: 0.5938 (p0) cc_final: 0.5508 (t0) REVERT: D 674 ASP cc_start: 0.5763 (OUTLIER) cc_final: 0.5052 (m-30) outliers start: 92 outliers final: 67 residues processed: 263 average time/residue: 0.2561 time to fit residues: 102.8929 Evaluate side-chains 244 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 172 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 581 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 613 ASP Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 145 optimal weight: 0.0970 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 503 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16468 Z= 0.182 Angle : 0.567 11.670 22339 Z= 0.291 Chirality : 0.044 0.161 2532 Planarity : 0.004 0.047 2945 Dihedral : 4.894 32.518 2257 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.28 % Allowed : 21.53 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -2.99 (0.17), residues: 2066 helix: -0.78 (0.24), residues: 478 sheet: -2.00 (0.30), residues: 258 loop : -2.60 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 444 HIS 0.006 0.001 HIS C 107 PHE 0.022 0.001 PHE A 230 TYR 0.011 0.001 TYR B 507 ARG 0.006 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 184 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7932 (t) REVERT: A 196 ASN cc_start: 0.7872 (t0) cc_final: 0.7518 (t0) REVERT: B 118 MET cc_start: 0.3466 (ptt) cc_final: 0.3151 (mtp) REVERT: B 455 MET cc_start: 0.6993 (ttm) cc_final: 0.6502 (ttp) REVERT: B 591 MET cc_start: 0.6543 (mmm) cc_final: 0.6204 (mtp) REVERT: B 653 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6470 (m-10) REVERT: B 659 ILE cc_start: 0.8836 (tp) cc_final: 0.8445 (tp) REVERT: B 691 ASP cc_start: 0.7750 (p0) cc_final: 0.7090 (p0) REVERT: D 19 ASP cc_start: 0.7110 (t0) cc_final: 0.6861 (t0) REVERT: D 222 LYS cc_start: 0.8091 (pttt) cc_final: 0.7723 (mttt) REVERT: D 444 TRP cc_start: 0.8050 (m-90) cc_final: 0.7843 (m-90) REVERT: D 451 TRP cc_start: 0.8912 (p90) cc_final: 0.8388 (p90) REVERT: D 565 ASN cc_start: 0.5763 (p0) cc_final: 0.5514 (t0) REVERT: D 674 ASP cc_start: 0.5211 (OUTLIER) cc_final: 0.4864 (m-30) REVERT: D 761 ILE cc_start: 0.4073 (OUTLIER) cc_final: 0.3417 (mp) outliers start: 74 outliers final: 58 residues processed: 247 average time/residue: 0.2634 time to fit residues: 99.4301 Evaluate side-chains 232 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 170 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 581 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 0.0970 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16468 Z= 0.143 Angle : 0.549 11.042 22339 Z= 0.279 Chirality : 0.043 0.159 2532 Planarity : 0.004 0.047 2945 Dihedral : 4.629 27.433 2257 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.05 % Allowed : 21.82 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: -2.79 (0.17), residues: 2066 helix: -0.56 (0.24), residues: 482 sheet: -1.93 (0.30), residues: 258 loop : -2.47 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 318 HIS 0.006 0.001 HIS C 107 PHE 0.025 0.001 PHE D 317 TYR 0.007 0.001 TYR B 507 ARG 0.008 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 188 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7949 (t) REVERT: A 181 GLN cc_start: 0.8263 (pp30) cc_final: 0.7883 (pt0) REVERT: B 455 MET cc_start: 0.6976 (ttm) cc_final: 0.6445 (ttp) REVERT: B 591 MET cc_start: 0.6547 (mmm) cc_final: 0.6170 (mtp) REVERT: B 653 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: B 659 ILE cc_start: 0.8808 (tp) cc_final: 0.8430 (tp) REVERT: B 691 ASP cc_start: 0.7684 (p0) cc_final: 0.7003 (p0) REVERT: C 179 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7584 (tttm) REVERT: D 19 ASP cc_start: 0.7070 (t0) cc_final: 0.6837 (t0) REVERT: D 137 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5545 (mp) REVERT: D 451 TRP cc_start: 0.8895 (p90) cc_final: 0.8382 (p90) REVERT: D 639 GLU cc_start: 0.6427 (tt0) cc_final: 0.6163 (tt0) outliers start: 70 outliers final: 53 residues processed: 246 average time/residue: 0.2648 time to fit residues: 99.8107 Evaluate side-chains 227 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 581 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 HIS ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 503 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16468 Z= 0.457 Angle : 0.760 12.121 22339 Z= 0.390 Chirality : 0.050 0.211 2532 Planarity : 0.005 0.054 2945 Dihedral : 5.678 36.954 2257 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 4.40 % Allowed : 21.82 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.22 (0.17), residues: 2066 helix: -1.17 (0.23), residues: 466 sheet: -2.04 (0.32), residues: 242 loop : -2.68 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 7 HIS 0.006 0.001 HIS A 107 PHE 0.029 0.003 PHE A 230 TYR 0.028 0.003 TYR B 507 ARG 0.007 0.001 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 179 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 182 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: B 1 MET cc_start: 0.4646 (ttt) cc_final: 0.4335 (ttt) REVERT: B 455 MET cc_start: 0.7102 (ttm) cc_final: 0.6600 (ttp) REVERT: B 653 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6998 (m-10) REVERT: B 691 ASP cc_start: 0.7785 (p0) cc_final: 0.7230 (p0) REVERT: B 703 PHE cc_start: 0.5710 (OUTLIER) cc_final: 0.3947 (m-80) REVERT: D 19 ASP cc_start: 0.7450 (t0) cc_final: 0.7202 (t0) REVERT: D 451 TRP cc_start: 0.8997 (p90) cc_final: 0.8425 (p90) REVERT: D 541 MET cc_start: 0.7750 (mtt) cc_final: 0.7549 (mtp) REVERT: D 674 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.4784 (m-30) REVERT: D 761 ILE cc_start: 0.3755 (OUTLIER) cc_final: 0.3180 (mp) outliers start: 76 outliers final: 59 residues processed: 240 average time/residue: 0.2625 time to fit residues: 97.0068 Evaluate side-chains 235 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 170 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 581 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 613 ASP Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 0.0670 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN C 217 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 16468 Z= 0.341 Angle : 0.934 59.197 22339 Z= 0.520 Chirality : 0.049 0.357 2532 Planarity : 0.006 0.170 2945 Dihedral : 5.651 36.530 2255 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.83 % Favored : 87.12 % Rotamer: Outliers : 4.05 % Allowed : 22.63 % Favored : 73.32 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.24 (0.17), residues: 2066 helix: -1.19 (0.23), residues: 466 sheet: -2.04 (0.32), residues: 242 loop : -2.69 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 7 HIS 0.273 0.005 HIS B 604 PHE 0.026 0.002 PHE A 230 TYR 0.027 0.002 TYR B 507 ARG 0.007 0.000 ARG D 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 171 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7873 (t) REVERT: B 1 MET cc_start: 0.4616 (ttt) cc_final: 0.4299 (ttt) REVERT: B 455 MET cc_start: 0.7081 (ttm) cc_final: 0.6585 (ttp) REVERT: B 604 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.5095 (m170) REVERT: B 653 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: B 691 ASP cc_start: 0.7759 (p0) cc_final: 0.7196 (p0) REVERT: B 703 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.3944 (m-80) REVERT: D 19 ASP cc_start: 0.7440 (t0) cc_final: 0.7191 (t0) REVERT: D 137 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5114 (mp) REVERT: D 451 TRP cc_start: 0.8972 (p90) cc_final: 0.8400 (p90) REVERT: D 674 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.4704 (m-30) REVERT: D 761 ILE cc_start: 0.3745 (OUTLIER) cc_final: 0.3172 (mp) outliers start: 70 outliers final: 57 residues processed: 229 average time/residue: 0.2566 time to fit residues: 90.1570 Evaluate side-chains 234 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 170 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 581 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 613 ASP Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 339 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.220835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.191511 restraints weight = 22023.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.191824 restraints weight = 25952.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.189177 restraints weight = 15551.497| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 16468 Z= 0.341 Angle : 0.934 59.197 22339 Z= 0.520 Chirality : 0.049 0.357 2532 Planarity : 0.006 0.170 2945 Dihedral : 5.651 36.530 2255 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.83 % Favored : 87.12 % Rotamer: Outliers : 3.70 % Allowed : 22.86 % Favored : 73.44 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.24 (0.17), residues: 2066 helix: -1.19 (0.23), residues: 466 sheet: -2.04 (0.32), residues: 242 loop : -2.69 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 7 HIS 0.273 0.005 HIS B 604 PHE 0.026 0.002 PHE A 230 TYR 0.027 0.002 TYR B 507 ARG 0.007 0.000 ARG D 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.42 seconds wall clock time: 57 minutes 42.51 seconds (3462.51 seconds total)