Starting phenix.real_space_refine on Mon Mar 18 10:53:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/03_2024/7q4d_13803_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/03_2024/7q4d_13803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/03_2024/7q4d_13803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/03_2024/7q4d_13803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/03_2024/7q4d_13803_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/03_2024/7q4d_13803_trim.pdb" } resolution = 3.78 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= 0.001 sd= 0.040 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 Zn 2 6.06 5 S 38 5.16 5 C 6772 2.51 5 N 1736 2.21 5 O 2088 1.98 5 H 9462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20098 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 9690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 9690 Classifications: {'peptide': 608} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 569} Chain: "B" Number of atoms: 9690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 9690 Classifications: {'peptide': 608} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 569} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.90, per 1000 atoms: 0.49 Number of scatterers: 20098 At special positions: 0 Unit cell: (101.76, 156.88, 93.28, 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 2 29.99 S 38 16.00 O 2088 8.00 N 1736 7.00 C 6772 6.00 H 9462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " distance=2.02 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 528 " distance=2.02 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 6 " " BMA E 3 " - " MAN E 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " BMA F 3 " - " MAN F 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN F 4 " - " NAG F 5 " " MAN L 4 " - " NAG L 5 " " MAN M 4 " - " NAG M 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " BETA1-6 " NAG C 1 " - " FUC C 7 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG M 1 " - " FUC M 7 " NAG-ASN " NAG A1302 " - " ASN A 416 " " NAG B1302 " - " ASN B 416 " " NAG C 1 " - " ASN A 289 " " NAG D 1 " - " ASN A 117 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 25 " " NAG G 1 " - " ASN A 480 " " NAG H 1 " - " ASN A 9 " " NAG I 1 " - " ASN A 82 " " NAG J 1 " - " ASN B 480 " " NAG K 1 " - " ASN B 45 " " NAG L 1 " - " ASN B 25 " " NAG M 1 " - " ASN B 289 " " NAG N 1 " - " ASN B 117 " " NAG O 1 " - " ASN B 82 " " NAG P 1 " - " ASN B 9 " Time building additional restraints: 18.19 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 365 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" NE2 HIS B 365 " 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 4 sheets defined 71.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.506A pdb=" N LEU A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 removed outlier: 3.891A pdb=" N LYS A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 124 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 170 through 190 removed outlier: 4.651A pdb=" N LEU A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.761A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 removed outlier: 3.552A pdb=" N GLU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 3.541A pdb=" N GLY A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 removed outlier: 3.951A pdb=" N GLY A 254 " --> pdb=" O HIS A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.622A pdb=" N PHE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.744A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 373 removed outlier: 3.595A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 386 through 401 removed outlier: 4.273A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 451 removed outlier: 4.021A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.604A pdb=" N LYS A 489 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.660A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.592A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 13 through 45 removed outlier: 3.631A pdb=" N LEU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 77 removed outlier: 3.680A pdb=" N LYS B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 124 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 170 through 190 removed outlier: 4.579A pdb=" N LEU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.724A pdb=" N TRP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 238 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 289 through 304 removed outlier: 3.649A pdb=" N PHE B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.807A pdb=" N TRP B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 373 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 386 through 401 removed outlier: 4.098A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.632A pdb=" N LYS B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 433 Processing helix chain 'B' and resid 434 through 451 removed outlier: 4.035A pdb=" N PHE B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 498 through 519 removed outlier: 3.649A pdb=" N PHE B 502 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.521A pdb=" N LYS B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 574 through 589 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 5.990A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 336 Processing sheet with id=AA3, first strand: chain 'B' and resid 248 through 249 removed outlier: 6.040A pdb=" N ILE B 248 " --> pdb=" O CYS B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 333 through 336 574 hydrogen bonds defined for protein. 1635 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: 6.44 Time building geometry restraints manager: 18.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9460 1.03 - 1.23: 76 1.23 - 1.42: 4775 1.42 - 1.62: 6037 1.62 - 1.82: 62 Bond restraints: 20410 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 MAN C 6 " pdb=" C2 MAN C 6 " ideal model delta sigma weight residual 1.526 1.573 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.360 0.046 2.00e-02 2.50e+03 5.36e+00 ... (remaining 20405 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.27: 229 104.27 - 111.71: 21772 111.71 - 119.14: 5189 119.14 - 126.57: 8955 126.57 - 134.01: 271 Bond angle restraints: 36416 Sorted by residual: angle pdb=" C3 MAN M 4 " pdb=" C2 MAN M 4 " pdb=" O2 MAN M 4 " ideal model delta sigma weight residual 111.77 96.84 14.93 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CA TYR A 372 " pdb=" CB TYR A 372 " pdb=" CG TYR A 372 " ideal model delta sigma weight residual 113.90 120.36 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " pdb=" CG GLU A 389 " ideal model delta sigma weight residual 114.10 106.95 7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" N LYS B 341 " pdb=" CA LYS B 341 " pdb=" C LYS B 341 " ideal model delta sigma weight residual 111.69 116.08 -4.39 1.23e+00 6.61e-01 1.28e+01 angle pdb=" CA ARG B 380 " pdb=" CB ARG B 380 " pdb=" CG ARG B 380 " ideal model delta sigma weight residual 114.10 106.98 7.12 2.00e+00 2.50e-01 1.27e+01 ... (remaining 36411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 9613 21.29 - 42.58: 541 42.58 - 63.88: 218 63.88 - 85.17: 95 85.17 - 106.46: 60 Dihedral angle restraints: 10527 sinusoidal: 6057 harmonic: 4470 Sorted by residual: dihedral pdb=" CA TRP B 594 " pdb=" C TRP B 594 " pdb=" N PRO B 595 " pdb=" CA PRO B 595 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PRO A 604 " pdb=" C PRO A 604 " pdb=" N ASP A 605 " pdb=" CA ASP A 605 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ALA A 383 " pdb=" C ALA A 383 " pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 10524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1585 0.094 - 0.189: 113 0.189 - 0.283: 7 0.283 - 0.377: 9 0.377 - 0.472: 2 Chirality restraints: 1716 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1713 not shown) Planarity restraints: 3008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 96 " -0.564 9.50e-02 1.11e+02 1.90e-01 5.27e+01 pdb=" NE ARG A 96 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 96 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 96 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 96 " 0.035 2.00e-02 2.50e+03 pdb="HH11 ARG A 96 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 96 " 0.042 2.00e-02 2.50e+03 pdb="HH21 ARG A 96 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 96 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 467 " -0.560 9.50e-02 1.11e+02 1.88e-01 4.60e+01 pdb=" NE ARG A 467 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 467 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG A 467 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 467 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 467 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 467 " -0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 467 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 467 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 413 " 0.223 9.50e-02 1.11e+02 8.53e-02 4.46e+01 pdb=" NE ARG B 413 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 413 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG B 413 " -0.087 2.00e-02 2.50e+03 pdb=" NH2 ARG B 413 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG B 413 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 413 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG B 413 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 413 " -0.011 2.00e-02 2.50e+03 ... (remaining 3005 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 954 2.19 - 2.79: 39398 2.79 - 3.39: 56661 3.39 - 4.00: 72443 4.00 - 4.60: 114237 Nonbonded interactions: 283693 Sorted by model distance: nonbonded pdb=" HE1 TRP B 464 " pdb=" OD2 ASP B 485 " model vdw 1.581 1.850 nonbonded pdb=" OD2 ASP B 443 " pdb=" H ILE B 499 " model vdw 1.593 1.850 nonbonded pdb=" HE1 TRP A 464 " pdb=" OD2 ASP A 485 " model vdw 1.596 1.850 nonbonded pdb=" HG1 THR B 291 " pdb=" OE2 GLU B 320 " model vdw 1.632 1.850 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.638 1.850 ... (remaining 283688 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' } ncs_group { reference = chain 'C' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'O' } 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: 3.030 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: 0.130 Extract box with map and model: 13.330 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 69.980 Find NCS groups from input model: 0.850 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.008 0.056 10948 Z= 0.495 Angle : 1.008 14.932 14920 Z= 0.500 Chirality : 0.056 0.472 1716 Planarity : 0.014 0.255 1854 Dihedral : 19.012 106.459 4824 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.89 (0.21), residues: 1212 helix: -1.26 (0.16), residues: 688 sheet: 0.48 (1.06), residues: 20 loop : -1.09 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 68 HIS 0.012 0.003 HIS B 526 PHE 0.022 0.003 PHE A 387 TYR 0.030 0.006 TYR A 369 ARG 0.042 0.004 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 559 MET cc_start: 0.8890 (ttt) cc_final: 0.8552 (ttt) REVERT: A 590 GLU cc_start: 0.7432 (tp30) cc_final: 0.6752 (tp30) REVERT: B 155 MET cc_start: 0.8621 (tpt) cc_final: 0.8331 (mmp) REVERT: B 431 GLU cc_start: 0.8374 (tt0) cc_final: 0.8166 (tt0) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.7481 time to fit residues: 132.3271 Evaluate side-chains 77 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A 588 ASN A 598 GLN B 112 ASN B 216 GLN B 292 HIS B 545 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10948 Z= 0.219 Angle : 0.754 7.416 14920 Z= 0.374 Chirality : 0.043 0.325 1716 Planarity : 0.006 0.054 1854 Dihedral : 14.126 81.451 2466 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.38 % Allowed : 5.07 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.06 (0.23), residues: 1212 helix: 0.34 (0.18), residues: 728 sheet: 1.23 (1.12), residues: 20 loop : -0.55 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 163 HIS 0.012 0.002 HIS B 361 PHE 0.019 0.002 PHE A 387 TYR 0.025 0.002 TYR A 372 ARG 0.006 0.001 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 MET cc_start: 0.8286 (tpt) cc_final: 0.8023 (mmp) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.5495 time to fit residues: 74.0821 Evaluate side-chains 79 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10948 Z= 0.264 Angle : 0.676 6.995 14920 Z= 0.336 Chirality : 0.041 0.308 1716 Planarity : 0.005 0.041 1854 Dihedral : 11.312 71.703 2466 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.48 % Allowed : 6.21 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.20 (0.23), residues: 1212 helix: 0.53 (0.18), residues: 736 sheet: 1.28 (1.13), residues: 20 loop : -0.40 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.011 0.002 HIS B 361 PHE 0.013 0.002 PHE A 178 TYR 0.022 0.002 TYR A 372 ARG 0.003 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 397 LEU cc_start: 0.8744 (tp) cc_final: 0.8479 (tt) REVERT: B 155 MET cc_start: 0.8279 (tpt) cc_final: 0.7823 (mmp) outliers start: 5 outliers final: 5 residues processed: 82 average time/residue: 0.6317 time to fit residues: 69.7416 Evaluate side-chains 78 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 588 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10948 Z= 0.201 Angle : 0.607 7.046 14920 Z= 0.302 Chirality : 0.038 0.280 1716 Planarity : 0.004 0.039 1854 Dihedral : 9.498 58.938 2466 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.67 % Allowed : 6.69 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1212 helix: 0.81 (0.18), residues: 734 sheet: 1.47 (1.16), residues: 20 loop : -0.23 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.009 0.001 HIS B 361 PHE 0.012 0.001 PHE A 178 TYR 0.020 0.002 TYR A 372 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 LEU cc_start: 0.8697 (tp) cc_final: 0.8497 (tt) outliers start: 7 outliers final: 7 residues processed: 81 average time/residue: 0.5506 time to fit residues: 61.7850 Evaluate side-chains 78 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10948 Z= 0.233 Angle : 0.594 7.154 14920 Z= 0.298 Chirality : 0.037 0.268 1716 Planarity : 0.004 0.038 1854 Dihedral : 8.259 59.189 2466 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.86 % Allowed : 7.93 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.74 (0.24), residues: 1212 helix: 0.95 (0.19), residues: 734 sheet: 1.47 (1.19), residues: 20 loop : -0.15 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.009 0.001 HIS B 361 PHE 0.012 0.001 PHE B 83 TYR 0.019 0.002 TYR A 372 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 MET cc_start: 0.7498 (ttm) cc_final: 0.7241 (ttm) REVERT: A 397 LEU cc_start: 0.8737 (tp) cc_final: 0.8509 (tt) REVERT: B 363 MET cc_start: 0.8449 (tmm) cc_final: 0.8061 (tmt) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.5545 time to fit residues: 63.9963 Evaluate side-chains 84 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10948 Z= 0.315 Angle : 0.631 7.395 14920 Z= 0.321 Chirality : 0.038 0.280 1716 Planarity : 0.004 0.041 1854 Dihedral : 7.995 58.501 2466 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.96 % Allowed : 8.32 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.58 (0.24), residues: 1212 helix: 0.85 (0.19), residues: 738 sheet: 1.40 (1.22), residues: 20 loop : -0.29 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.009 0.002 HIS A 404 PHE 0.023 0.002 PHE B 83 TYR 0.020 0.002 TYR A 175 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 LEU cc_start: 0.8740 (tp) cc_final: 0.8525 (tt) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.5483 time to fit residues: 62.4765 Evaluate side-chains 80 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10948 Z= 0.171 Angle : 0.559 7.117 14920 Z= 0.278 Chirality : 0.036 0.256 1716 Planarity : 0.004 0.057 1854 Dihedral : 7.404 58.527 2466 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.15 % Allowed : 8.22 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1212 helix: 1.19 (0.19), residues: 738 sheet: 1.10 (1.21), residues: 20 loop : -0.12 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.007 0.001 HIS B 361 PHE 0.012 0.001 PHE A 178 TYR 0.017 0.001 TYR A 372 ARG 0.004 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 267 MET cc_start: 0.8023 (ttm) cc_final: 0.7772 (ttm) REVERT: B 363 MET cc_start: 0.8465 (tmm) cc_final: 0.7992 (tmm) REVERT: B 606 ASN cc_start: 0.7466 (m-40) cc_final: 0.6860 (t0) outliers start: 12 outliers final: 12 residues processed: 84 average time/residue: 0.5291 time to fit residues: 62.7850 Evaluate side-chains 84 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10948 Z= 0.249 Angle : 0.583 7.304 14920 Z= 0.294 Chirality : 0.036 0.255 1716 Planarity : 0.004 0.036 1854 Dihedral : 7.279 59.650 2466 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.24 % Allowed : 8.80 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.94 (0.24), residues: 1212 helix: 1.17 (0.19), residues: 738 sheet: 1.04 (1.22), residues: 20 loop : -0.18 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.011 0.001 HIS A 512 PHE 0.012 0.001 PHE A 178 TYR 0.018 0.002 TYR A 372 ARG 0.003 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 267 MET cc_start: 0.8051 (ttm) cc_final: 0.7758 (ttm) REVERT: B 363 MET cc_start: 0.8517 (tmm) cc_final: 0.8096 (tmm) outliers start: 13 outliers final: 13 residues processed: 80 average time/residue: 0.5008 time to fit residues: 56.2600 Evaluate side-chains 84 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10948 Z= 0.180 Angle : 0.544 7.046 14920 Z= 0.272 Chirality : 0.035 0.240 1716 Planarity : 0.004 0.033 1854 Dihedral : 6.827 59.862 2466 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.15 % Allowed : 8.89 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.20 (0.24), residues: 1212 helix: 1.39 (0.19), residues: 738 sheet: 0.79 (1.23), residues: 20 loop : -0.08 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.008 0.001 HIS B 361 PHE 0.011 0.001 PHE A 178 TYR 0.016 0.001 TYR A 372 ARG 0.003 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 267 MET cc_start: 0.8094 (ttm) cc_final: 0.7822 (ttm) REVERT: B 363 MET cc_start: 0.8471 (tmm) cc_final: 0.8016 (tmm) REVERT: B 606 ASN cc_start: 0.7469 (m-40) cc_final: 0.6857 (t0) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.5328 time to fit residues: 62.1478 Evaluate side-chains 82 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10948 Z= 0.180 Angle : 0.534 7.028 14920 Z= 0.268 Chirality : 0.034 0.238 1716 Planarity : 0.004 0.032 1854 Dihedral : 6.449 58.501 2466 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.15 % Allowed : 8.89 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.28 (0.24), residues: 1212 helix: 1.44 (0.19), residues: 752 sheet: 0.69 (1.27), residues: 20 loop : -0.05 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.008 0.001 HIS B 361 PHE 0.048 0.001 PHE A 33 TYR 0.016 0.001 TYR A 372 ARG 0.004 0.000 ARG B 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8106 (ttm) cc_final: 0.7848 (ttm) REVERT: B 164 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7299 (m90) REVERT: B 363 MET cc_start: 0.8458 (tmm) cc_final: 0.8048 (tmm) REVERT: B 606 ASN cc_start: 0.7410 (m-40) cc_final: 0.6836 (t0) outliers start: 12 outliers final: 11 residues processed: 81 average time/residue: 0.5090 time to fit residues: 58.6863 Evaluate side-chains 82 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.0770 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077246 restraints weight = 78581.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080364 restraints weight = 33887.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082445 restraints weight = 19319.357| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10948 Z= 0.167 Angle : 0.525 6.877 14920 Z= 0.263 Chirality : 0.034 0.235 1716 Planarity : 0.004 0.031 1854 Dihedral : 6.289 57.960 2466 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.24 % Allowed : 8.51 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.41 (0.25), residues: 1212 helix: 1.52 (0.19), residues: 758 sheet: 0.65 (1.30), residues: 20 loop : 0.02 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.008 0.001 HIS B 361 PHE 0.021 0.001 PHE A 33 TYR 0.015 0.001 TYR A 372 ARG 0.003 0.000 ARG B 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3793.97 seconds wall clock time: 68 minutes 46.45 seconds (4126.45 seconds total)