Starting phenix.real_space_refine on Mon Feb 19 03:09:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxd_30905/02_2024/7dxd_30905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxd_30905/02_2024/7dxd_30905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxd_30905/02_2024/7dxd_30905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxd_30905/02_2024/7dxd_30905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxd_30905/02_2024/7dxd_30905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxd_30905/02_2024/7dxd_30905.pdb" } resolution = 3.9 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= 0.013 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 S 132 5.16 5 C 15424 2.51 5 N 3792 2.21 5 O 4272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B GLU 789": "OE1" <-> "OE2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ASP 394": "OD1" <-> "OD2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 632": "OE1" <-> "OE2" Residue "C GLU 664": "OE1" <-> "OE2" Residue "C GLU 672": "OE1" <-> "OE2" Residue "C GLU 789": "OE1" <-> "OE2" Residue "C GLU 808": "OE1" <-> "OE2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ASP 394": "OD1" <-> "OD2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D GLU 447": "OE1" <-> "OE2" Residue "D ARG 450": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 540": "NH1" <-> "NH2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 632": "OE1" <-> "OE2" Residue "D GLU 664": "OE1" <-> "OE2" Residue "D GLU 672": "OE1" <-> "OE2" Residue "D GLU 789": "OE1" <-> "OE2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D GLU 816": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5870 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5870 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5870 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5870 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1328 SG CYS A 182 86.403 24.516 78.918 1.00143.63 S ATOM 1343 SG CYS A 184 88.739 23.851 76.056 1.00140.89 S ATOM 1361 SG CYS A 187 87.488 27.317 76.638 1.00138.90 S ATOM 7198 SG CYS B 182 98.798 86.400 78.920 1.00143.63 S ATOM 7213 SG CYS B 184 99.463 88.736 76.058 1.00140.89 S ATOM 7231 SG CYS B 187 95.997 87.485 76.640 1.00138.90 S ATOM 13068 SG CYS C 182 24.519 36.912 78.913 1.00143.63 S ATOM 13083 SG CYS C 184 23.854 34.576 76.051 1.00140.89 S ATOM 13101 SG CYS C 187 27.320 35.827 76.634 1.00138.90 S ATOM 18938 SG CYS D 182 36.914 98.795 78.915 1.00143.63 S ATOM 18953 SG CYS D 184 34.579 99.460 76.053 1.00140.89 S ATOM 18971 SG CYS D 187 35.830 95.994 76.635 1.00138.90 S Time building chain proxies: 12.47, per 1000 atoms: 0.53 Number of scatterers: 23628 At special positions: 0 Unit cell: (124.355, 124.355, 167.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 132 16.00 O 4272 8.00 N 3792 7.00 C 15424 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: 10.15 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" ND1 HIS A 178 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 182 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 184 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 187 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" ND1 HIS B 178 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 182 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 184 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 187 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" ND1 HIS C 178 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 182 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 184 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 187 " pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" ND1 HIS D 178 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 182 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 184 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 187 " Number of angles added : 12 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 0 sheets defined 77.5% alpha, 0.0% 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 25 through 37 Processing helix chain 'A' and resid 39 through 50 Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.928A pdb=" N GLN A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.971A pdb=" N SER A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 240 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.601A pdb=" N ARG A 330 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 358 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 423 through 448 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.644A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 493 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 539 through 548 removed outlier: 4.149A pdb=" N LEU A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 551 through 588 removed outlier: 4.683A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.770A pdb=" N SER A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 622 " --> pdb=" O VAL A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 622' Processing helix chain 'A' and resid 628 through 663 Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 788 through 824 removed outlier: 3.713A pdb=" N ILE A 795 " --> pdb=" O GLU A 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.928A pdb=" N GLN B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.970A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 Processing helix chain 'B' and resid 243 through 264 removed outlier: 3.613A pdb=" N LEU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.601A pdb=" N ARG B 330 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 358 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 423 through 448 Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.644A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 493 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 521 through 538 Processing helix chain 'B' and resid 539 through 548 removed outlier: 4.150A pdb=" N LEU B 545 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Proline residue: B 546 - end of helix Processing helix chain 'B' and resid 551 through 588 removed outlier: 4.683A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 618 through 622 removed outlier: 3.769A pdb=" N SER B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 622' Processing helix chain 'B' and resid 628 through 663 Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 761 through 784 Processing helix chain 'B' and resid 788 through 824 removed outlier: 3.712A pdb=" N ILE B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 39 through 50 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 74 through 83 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 124 through 131 removed outlier: 3.929A pdb=" N GLN C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 196 through 210 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.970A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 240 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.613A pdb=" N LEU C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.601A pdb=" N ARG C 330 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 358 Proline residue: C 349 - end of helix Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 423 through 448 Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.644A pdb=" N LEU C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 493 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 521 through 538 Processing helix chain 'C' and resid 539 through 548 removed outlier: 4.150A pdb=" N LEU C 545 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Proline residue: C 546 - end of helix Processing helix chain 'C' and resid 551 through 588 removed outlier: 4.682A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 618 through 622 removed outlier: 3.768A pdb=" N SER C 621 " --> pdb=" O GLU C 618 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 622 " --> pdb=" O VAL C 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 618 through 622' Processing helix chain 'C' and resid 628 through 663 Processing helix chain 'C' and resid 669 through 683 Processing helix chain 'C' and resid 761 through 784 Processing helix chain 'C' and resid 788 through 824 removed outlier: 3.712A pdb=" N ILE C 795 " --> pdb=" O GLU C 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 39 through 50 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 74 through 83 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 124 through 131 removed outlier: 3.929A pdb=" N GLN D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.971A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.613A pdb=" N LEU D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.600A pdb=" N ARG D 330 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 358 Proline residue: D 349 - end of helix Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 423 through 448 Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.643A pdb=" N LEU D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 493 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 521 through 538 Processing helix chain 'D' and resid 539 through 548 removed outlier: 4.150A pdb=" N LEU D 545 " --> pdb=" O ALA D 542 " (cutoff:3.500A) Proline residue: D 546 - end of helix Processing helix chain 'D' and resid 551 through 588 removed outlier: 4.683A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 618 through 622 removed outlier: 3.769A pdb=" N SER D 621 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 622 " --> pdb=" O VAL D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 622' Processing helix chain 'D' and resid 628 through 663 Processing helix chain 'D' and resid 669 through 683 Processing helix chain 'D' and resid 761 through 784 Processing helix chain 'D' and resid 788 through 824 removed outlier: 3.712A pdb=" N ILE D 795 " --> pdb=" O GLU D 791 " (cutoff:3.500A) 1600 hydrogen bonds defined for protein. 4740 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: 7.55 Time building geometry restraints manager: 10.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7376 1.34 - 1.47: 5776 1.47 - 1.59: 10776 1.59 - 1.72: 4 1.72 - 1.84: 216 Bond restraints: 24148 Sorted by residual: bond pdb=" CAY Y01 B 901 " pdb=" OAW Y01 B 901 " ideal model delta sigma weight residual 1.332 1.466 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" CAY Y01 A 901 " pdb=" OAW Y01 A 901 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" CAY Y01 C 901 " pdb=" OAW Y01 C 901 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" CAY Y01 D 901 " pdb=" OAW Y01 D 901 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" CAX Y01 B 901 " pdb=" OAH Y01 B 901 " ideal model delta sigma weight residual 1.248 1.330 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 24143 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.80: 388 104.80 - 112.11: 12060 112.11 - 119.42: 7806 119.42 - 126.73: 12192 126.73 - 134.04: 278 Bond angle restraints: 32724 Sorted by residual: angle pdb=" C LEU B 24 " pdb=" CA LEU B 24 " pdb=" CB LEU B 24 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" C LEU A 24 " pdb=" CA LEU A 24 " pdb=" CB LEU A 24 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" C LEU C 24 " pdb=" CA LEU C 24 " pdb=" CB LEU C 24 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" C LEU D 24 " pdb=" CA LEU D 24 " pdb=" CB LEU D 24 " ideal model delta sigma weight residual 116.54 110.58 5.96 1.15e+00 7.56e-01 2.68e+01 angle pdb=" CA LEU D 24 " pdb=" C LEU D 24 " pdb=" N THR D 25 " ideal model delta sigma weight residual 119.52 115.45 4.07 7.90e-01 1.60e+00 2.65e+01 ... (remaining 32719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 13244 16.23 - 32.46: 1076 32.46 - 48.69: 228 48.69 - 64.92: 92 64.92 - 81.15: 24 Dihedral angle restraints: 14664 sinusoidal: 6024 harmonic: 8640 Sorted by residual: dihedral pdb=" CA ILE B 174 " pdb=" C ILE B 174 " pdb=" N GLU B 175 " pdb=" CA GLU B 175 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ILE A 174 " pdb=" C ILE A 174 " pdb=" N GLU A 175 " pdb=" CA GLU A 175 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ILE C 174 " pdb=" C ILE C 174 " pdb=" N GLU C 175 " pdb=" CA GLU C 175 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 14661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3268 0.058 - 0.116: 439 0.116 - 0.173: 17 0.173 - 0.231: 4 0.231 - 0.289: 4 Chirality restraints: 3732 Sorted by residual: chirality pdb=" CB ILE A 655 " pdb=" CA ILE A 655 " pdb=" CG1 ILE A 655 " pdb=" CG2 ILE A 655 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE B 655 " pdb=" CA ILE B 655 " pdb=" CG1 ILE B 655 " pdb=" CG2 ILE B 655 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE C 655 " pdb=" CA ILE C 655 " pdb=" CG1 ILE C 655 " pdb=" CG2 ILE C 655 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 3729 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 656 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ALA B 656 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA B 656 " -0.011 2.00e-02 2.50e+03 pdb=" N MET B 657 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 656 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ALA C 656 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA C 656 " 0.011 2.00e-02 2.50e+03 pdb=" N MET C 657 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 656 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ALA A 656 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA A 656 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 657 " 0.010 2.00e-02 2.50e+03 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5500 2.79 - 3.32: 23849 3.32 - 3.84: 39439 3.84 - 4.37: 45856 4.37 - 4.90: 77826 Nonbonded interactions: 192470 Sorted by model distance: nonbonded pdb=" O TYR C 214 " pdb=" OG SER C 218 " model vdw 2.260 2.440 nonbonded pdb=" O TYR B 214 " pdb=" OG SER B 218 " model vdw 2.260 2.440 nonbonded pdb=" O TYR D 214 " pdb=" OG SER D 218 " model vdw 2.260 2.440 nonbonded pdb=" O TYR A 214 " pdb=" OG SER A 218 " model vdw 2.260 2.440 nonbonded pdb=" NZ LYS B 306 " pdb=" OE2 GLU B 672 " model vdw 2.299 2.520 ... (remaining 192465 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 'B' selection = chain 'C' selection = chain 'D' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.920 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 66.420 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.140 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 24148 Z= 0.226 Angle : 0.629 10.145 32724 Z= 0.340 Chirality : 0.039 0.289 3732 Planarity : 0.004 0.035 4076 Dihedral : 13.513 81.154 9056 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 6.27 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 2880 helix: 0.09 (0.10), residues: 2044 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 611 HIS 0.002 0.001 HIS B 311 PHE 0.009 0.001 PHE C 381 TYR 0.012 0.001 TYR C 639 ARG 0.003 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 369 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9152 (ttp) cc_final: 0.8623 (tmm) REVERT: B 15 PHE cc_start: 0.6702 (m-10) cc_final: 0.6493 (m-80) REVERT: B 464 MET cc_start: 0.9151 (ttp) cc_final: 0.8625 (tmm) REVERT: C 464 MET cc_start: 0.9151 (ttp) cc_final: 0.8627 (tmm) REVERT: D 15 PHE cc_start: 0.6710 (m-10) cc_final: 0.6496 (m-80) REVERT: D 464 MET cc_start: 0.9152 (ttp) cc_final: 0.8625 (tmm) outliers start: 32 outliers final: 0 residues processed: 393 average time/residue: 0.3520 time to fit residues: 220.8050 Evaluate side-chains 178 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 265 optimal weight: 7.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 659 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 659 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN C 659 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN D 659 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24148 Z= 0.246 Angle : 0.583 8.309 32724 Z= 0.304 Chirality : 0.039 0.139 3732 Planarity : 0.004 0.041 4076 Dihedral : 5.897 55.157 3432 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.29 % Allowed : 8.82 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 2880 helix: 1.52 (0.11), residues: 2088 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 322 HIS 0.003 0.001 HIS B 311 PHE 0.025 0.002 PHE A 15 TYR 0.015 0.001 TYR A 138 ARG 0.002 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 175 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.9085 (mmm) cc_final: 0.8880 (mmm) REVERT: A 252 MET cc_start: 0.8466 (tpp) cc_final: 0.8210 (tpp) REVERT: A 313 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8835 (m-40) REVERT: A 464 MET cc_start: 0.9128 (ttp) cc_final: 0.8627 (tmm) REVERT: A 572 PHE cc_start: 0.7892 (t80) cc_final: 0.5850 (t80) REVERT: A 652 ASN cc_start: 0.8810 (t0) cc_final: 0.8590 (t0) REVERT: B 169 MET cc_start: 0.9085 (mmm) cc_final: 0.8885 (mmm) REVERT: B 252 MET cc_start: 0.8466 (tpp) cc_final: 0.8203 (tpp) REVERT: B 313 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8837 (m-40) REVERT: B 464 MET cc_start: 0.9138 (ttp) cc_final: 0.8632 (tmm) REVERT: B 572 PHE cc_start: 0.7895 (t80) cc_final: 0.5857 (t80) REVERT: B 652 ASN cc_start: 0.8824 (t0) cc_final: 0.8603 (t0) REVERT: C 169 MET cc_start: 0.9079 (mmm) cc_final: 0.8877 (mmm) REVERT: C 313 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8836 (m-40) REVERT: C 464 MET cc_start: 0.9129 (ttp) cc_final: 0.8630 (tmm) REVERT: C 572 PHE cc_start: 0.7894 (t80) cc_final: 0.5842 (t80) REVERT: C 652 ASN cc_start: 0.8750 (t0) cc_final: 0.8546 (t0) REVERT: D 169 MET cc_start: 0.9082 (mmm) cc_final: 0.8879 (mmm) REVERT: D 252 MET cc_start: 0.8476 (tpp) cc_final: 0.8221 (tpp) REVERT: D 313 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8841 (m-40) REVERT: D 464 MET cc_start: 0.9138 (ttp) cc_final: 0.8631 (tmm) REVERT: D 572 PHE cc_start: 0.7900 (t80) cc_final: 0.5846 (t80) REVERT: D 652 ASN cc_start: 0.8742 (t0) cc_final: 0.8538 (t0) outliers start: 84 outliers final: 44 residues processed: 251 average time/residue: 0.2791 time to fit residues: 120.5003 Evaluate side-chains 187 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 139 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24148 Z= 0.248 Angle : 0.555 6.948 32724 Z= 0.288 Chirality : 0.038 0.138 3732 Planarity : 0.004 0.043 4076 Dihedral : 5.841 52.126 3432 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.43 % Allowed : 10.11 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 2880 helix: 2.10 (0.11), residues: 2124 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 322 HIS 0.004 0.001 HIS C 165 PHE 0.012 0.001 PHE B 15 TYR 0.017 0.001 TYR B 37 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 140 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9111 (ttp) cc_final: 0.8682 (tmm) REVERT: B 464 MET cc_start: 0.9118 (ttp) cc_final: 0.8680 (tmm) REVERT: C 464 MET cc_start: 0.9110 (ttp) cc_final: 0.8687 (tmm) REVERT: D 464 MET cc_start: 0.9116 (ttp) cc_final: 0.8675 (tmm) outliers start: 62 outliers final: 24 residues processed: 196 average time/residue: 0.3156 time to fit residues: 104.5986 Evaluate side-chains 146 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 0.0370 chunk 178 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 chunk 139 optimal weight: 0.2980 chunk 252 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN C 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24148 Z= 0.138 Angle : 0.509 8.673 32724 Z= 0.260 Chirality : 0.037 0.125 3732 Planarity : 0.004 0.039 4076 Dihedral : 5.872 55.237 3432 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.53 % Allowed : 11.99 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2880 helix: 2.48 (0.11), residues: 2112 sheet: None (None), residues: 0 loop : -1.01 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 673 HIS 0.001 0.000 HIS B 198 PHE 0.013 0.001 PHE C 568 TYR 0.011 0.001 TYR D 138 ARG 0.001 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.9475 (mm) cc_final: 0.9267 (tt) REVERT: A 430 MET cc_start: 0.8408 (tmm) cc_final: 0.8152 (tmm) REVERT: A 464 MET cc_start: 0.9064 (ttp) cc_final: 0.8436 (tmm) REVERT: A 572 PHE cc_start: 0.8140 (t80) cc_final: 0.7627 (t80) REVERT: A 805 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8654 (mm-30) REVERT: B 274 ILE cc_start: 0.9474 (mm) cc_final: 0.9267 (tt) REVERT: B 464 MET cc_start: 0.9065 (ttp) cc_final: 0.8435 (tmm) REVERT: B 572 PHE cc_start: 0.8130 (t80) cc_final: 0.7612 (t80) REVERT: B 659 ASN cc_start: 0.8757 (m110) cc_final: 0.8244 (m110) REVERT: C 430 MET cc_start: 0.8405 (tmm) cc_final: 0.8148 (tmm) REVERT: C 464 MET cc_start: 0.9063 (ttp) cc_final: 0.8438 (tmm) REVERT: C 572 PHE cc_start: 0.8130 (t80) cc_final: 0.7613 (t80) REVERT: D 274 ILE cc_start: 0.9474 (mm) cc_final: 0.9274 (tt) REVERT: D 464 MET cc_start: 0.9065 (ttp) cc_final: 0.8435 (tmm) REVERT: D 572 PHE cc_start: 0.8137 (t80) cc_final: 0.7617 (t80) outliers start: 39 outliers final: 28 residues processed: 184 average time/residue: 0.2952 time to fit residues: 93.3438 Evaluate side-chains 159 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24148 Z= 0.181 Angle : 0.498 7.982 32724 Z= 0.254 Chirality : 0.037 0.130 3732 Planarity : 0.004 0.039 4076 Dihedral : 5.834 56.779 3432 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 12.62 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.16), residues: 2880 helix: 2.59 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 322 HIS 0.002 0.001 HIS A 311 PHE 0.026 0.001 PHE C 568 TYR 0.012 0.001 TYR B 37 ARG 0.002 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 130 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8439 (tmm) cc_final: 0.8128 (tmm) REVERT: A 464 MET cc_start: 0.9093 (ttp) cc_final: 0.8437 (tmm) REVERT: B 139 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7425 (p0) REVERT: B 464 MET cc_start: 0.9113 (ttp) cc_final: 0.8458 (tmm) REVERT: B 655 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9402 (mt) REVERT: B 659 ASN cc_start: 0.8726 (m110) cc_final: 0.8242 (m110) REVERT: C 427 MET cc_start: 0.8935 (mmm) cc_final: 0.8583 (mmp) REVERT: C 430 MET cc_start: 0.8436 (tmm) cc_final: 0.8129 (tmm) REVERT: C 464 MET cc_start: 0.9095 (ttp) cc_final: 0.8436 (tmm) REVERT: D 139 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7420 (p0) REVERT: D 464 MET cc_start: 0.9116 (ttp) cc_final: 0.8459 (tmm) outliers start: 53 outliers final: 24 residues processed: 179 average time/residue: 0.2966 time to fit residues: 92.2492 Evaluate side-chains 151 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24148 Z= 0.207 Angle : 0.500 7.047 32724 Z= 0.260 Chirality : 0.037 0.133 3732 Planarity : 0.004 0.039 4076 Dihedral : 5.847 57.135 3432 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.31 % Allowed : 12.50 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.16), residues: 2880 helix: 2.61 (0.11), residues: 2124 sheet: None (None), residues: 0 loop : -0.72 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 322 HIS 0.003 0.001 HIS C 165 PHE 0.029 0.001 PHE A 568 TYR 0.013 0.001 TYR C 60 ARG 0.002 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 129 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7534 (p0) REVERT: A 427 MET cc_start: 0.8805 (mmt) cc_final: 0.8448 (mmt) REVERT: A 430 MET cc_start: 0.8468 (tmm) cc_final: 0.8139 (tmm) REVERT: A 464 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8442 (tmm) REVERT: A 568 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: B 139 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7540 (p0) REVERT: B 427 MET cc_start: 0.8892 (mmt) cc_final: 0.8692 (mmt) REVERT: B 464 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8428 (tmm) REVERT: C 139 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7524 (p0) REVERT: C 430 MET cc_start: 0.8461 (tmm) cc_final: 0.8129 (tmm) REVERT: C 464 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8434 (tmm) REVERT: D 139 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7538 (p0) REVERT: D 464 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8430 (tmm) outliers start: 59 outliers final: 28 residues processed: 172 average time/residue: 0.2854 time to fit residues: 84.0640 Evaluate side-chains 161 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24148 Z= 0.256 Angle : 0.535 8.589 32724 Z= 0.279 Chirality : 0.038 0.139 3732 Planarity : 0.004 0.039 4076 Dihedral : 5.899 56.587 3432 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.47 % Allowed : 12.19 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.16), residues: 2880 helix: 2.52 (0.11), residues: 2124 sheet: None (None), residues: 0 loop : -0.66 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 432 HIS 0.005 0.001 HIS C 165 PHE 0.034 0.001 PHE A 568 TYR 0.015 0.001 TYR C 60 ARG 0.003 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 126 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7667 (p0) REVERT: A 427 MET cc_start: 0.8814 (mmt) cc_final: 0.8516 (mmt) REVERT: A 430 MET cc_start: 0.8472 (tmm) cc_final: 0.8115 (tmm) REVERT: A 464 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8493 (tmm) REVERT: B 139 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.7670 (p0) REVERT: B 464 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8474 (tmm) REVERT: C 139 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7665 (p0) REVERT: C 427 MET cc_start: 0.8865 (mmt) cc_final: 0.8609 (mmt) REVERT: C 430 MET cc_start: 0.8468 (tmm) cc_final: 0.8093 (tmm) REVERT: C 464 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8483 (tmm) REVERT: D 139 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7669 (p0) REVERT: D 464 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8478 (tmm) outliers start: 63 outliers final: 28 residues processed: 171 average time/residue: 0.2947 time to fit residues: 85.9748 Evaluate side-chains 155 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 221 optimal weight: 0.0470 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24148 Z= 0.179 Angle : 0.508 8.057 32724 Z= 0.265 Chirality : 0.038 0.208 3732 Planarity : 0.004 0.039 4076 Dihedral : 5.923 57.169 3432 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.65 % Allowed : 13.36 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.16), residues: 2880 helix: 2.50 (0.11), residues: 2148 sheet: None (None), residues: 0 loop : -0.90 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 432 HIS 0.002 0.001 HIS D 311 PHE 0.038 0.001 PHE B 568 TYR 0.012 0.001 TYR A 60 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 138 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7676 (p0) REVERT: A 427 MET cc_start: 0.8818 (mmt) cc_final: 0.8501 (mmt) REVERT: A 430 MET cc_start: 0.8480 (tmm) cc_final: 0.8117 (tmm) REVERT: A 464 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8456 (tmm) REVERT: B 139 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7611 (p0) REVERT: B 464 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8430 (tmm) REVERT: C 139 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7670 (p0) REVERT: C 427 MET cc_start: 0.8796 (mmt) cc_final: 0.8519 (mmt) REVERT: C 430 MET cc_start: 0.8459 (tmm) cc_final: 0.8105 (tmm) REVERT: C 464 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8437 (tmm) REVERT: D 139 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7619 (p0) REVERT: D 464 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8432 (tmm) outliers start: 42 outliers final: 29 residues processed: 169 average time/residue: 0.3209 time to fit residues: 90.2805 Evaluate side-chains 162 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 262 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 261 optimal weight: 0.0010 overall best weight: 3.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24148 Z= 0.274 Angle : 0.575 9.148 32724 Z= 0.297 Chirality : 0.039 0.160 3732 Planarity : 0.004 0.039 4076 Dihedral : 5.926 55.977 3432 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.68 % Allowed : 13.91 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.16), residues: 2880 helix: 2.45 (0.11), residues: 2152 sheet: None (None), residues: 0 loop : -0.95 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 438 HIS 0.003 0.001 HIS B 311 PHE 0.038 0.002 PHE B 568 TYR 0.012 0.001 TYR B 37 ARG 0.003 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7661 (p0) REVERT: A 427 MET cc_start: 0.8809 (mmt) cc_final: 0.8609 (mmt) REVERT: A 430 MET cc_start: 0.8481 (tmm) cc_final: 0.8113 (tmm) REVERT: A 464 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8523 (tmm) REVERT: A 538 PHE cc_start: 0.8785 (m-80) cc_final: 0.8559 (m-80) REVERT: B 139 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7665 (p0) REVERT: B 464 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8495 (tmm) REVERT: C 139 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.7659 (p0) REVERT: C 169 MET cc_start: 0.8907 (mmm) cc_final: 0.8704 (mmm) REVERT: C 430 MET cc_start: 0.8465 (tmm) cc_final: 0.8103 (tmm) REVERT: C 464 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8461 (tmm) REVERT: D 139 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7672 (p0) REVERT: D 169 MET cc_start: 0.8907 (mmm) cc_final: 0.8703 (mmm) REVERT: D 464 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8501 (tmm) outliers start: 43 outliers final: 26 residues processed: 152 average time/residue: 0.3105 time to fit residues: 81.0740 Evaluate side-chains 153 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 568 PHE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 267 optimal weight: 0.3980 chunk 231 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24148 Z= 0.166 Angle : 0.549 10.438 32724 Z= 0.283 Chirality : 0.038 0.231 3732 Planarity : 0.004 0.040 4076 Dihedral : 5.900 56.233 3432 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.33 % Allowed : 14.58 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.16), residues: 2880 helix: 2.53 (0.11), residues: 2152 sheet: None (None), residues: 0 loop : -0.94 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 432 HIS 0.002 0.000 HIS C 311 PHE 0.032 0.001 PHE D 568 TYR 0.011 0.001 TYR D 138 ARG 0.001 0.000 ARG A 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8170 (mpp) cc_final: 0.7897 (mpp) REVERT: A 139 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7682 (p0) REVERT: A 430 MET cc_start: 0.8464 (tmm) cc_final: 0.8102 (tmm) REVERT: A 464 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8524 (tmm) REVERT: B 61 MET cc_start: 0.8200 (mpp) cc_final: 0.7905 (mpp) REVERT: B 464 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8463 (tmm) REVERT: C 61 MET cc_start: 0.8157 (mpp) cc_final: 0.7881 (mpp) REVERT: C 139 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7678 (p0) REVERT: C 169 MET cc_start: 0.8893 (mmm) cc_final: 0.8686 (mmm) REVERT: C 427 MET cc_start: 0.8880 (mmt) cc_final: 0.8499 (mmt) REVERT: C 430 MET cc_start: 0.8430 (tmm) cc_final: 0.8080 (tmm) REVERT: C 464 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8466 (tmm) REVERT: D 61 MET cc_start: 0.8196 (mpp) cc_final: 0.7900 (mpp) REVERT: D 169 MET cc_start: 0.8898 (mmm) cc_final: 0.8687 (mmm) REVERT: D 464 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8481 (tmm) outliers start: 34 outliers final: 24 residues processed: 155 average time/residue: 0.2828 time to fit residues: 75.4473 Evaluate side-chains 154 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 238 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.063570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050952 restraints weight = 98356.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052661 restraints weight = 55000.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053853 restraints weight = 37616.568| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24148 Z= 0.150 Angle : 0.551 10.366 32724 Z= 0.281 Chirality : 0.037 0.206 3732 Planarity : 0.004 0.039 4076 Dihedral : 5.935 57.996 3432 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.29 % Allowed : 14.69 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.16), residues: 2880 helix: 2.55 (0.11), residues: 2148 sheet: None (None), residues: 0 loop : -0.87 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 432 HIS 0.001 0.000 HIS B 377 PHE 0.028 0.001 PHE C 568 TYR 0.011 0.001 TYR A 138 ARG 0.001 0.000 ARG D 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3419.79 seconds wall clock time: 64 minutes 18.08 seconds (3858.08 seconds total)