Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 17:47:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/04_2023/7q4d_13803_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/04_2023/7q4d_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_13803/04_2023/7q4d_13803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/04_2023/7q4d_13803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/04_2023/7q4d_13803_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4d_13803/04_2023/7q4d_13803_trim.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 8.80, per 1000 atoms: 0.44 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 1.7 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: 0.64 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: 7.32 Time building geometry restraints manager: 18.63 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 - 17.49: 7341 17.49 - 34.98: 499 34.98 - 52.48: 93 52.48 - 69.97: 82 69.97 - 87.46: 16 Dihedral angle restraints: 8031 sinusoidal: 3561 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 8028 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 11.610 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 70.410 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.160 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- 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 : 13.700 87.462 3696 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 % 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 *********************** 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 : 1.629 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 outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.7824 time to fit residues: 138.6777 Evaluate side-chains 76 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2870 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 545 GLN A 588 ASN A 598 GLN B 112 ASN B 216 GLN B 545 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 10948 Z= 0.239 Angle : 0.736 7.494 14920 Z= 0.376 Chirality : 0.039 0.284 1716 Planarity : 0.006 0.067 1854 Dihedral : 5.547 20.755 1338 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.38 % 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: -0.21 (0.22), residues: 1212 helix: 0.23 (0.18), residues: 728 sheet: 1.16 (1.11), residues: 20 loop : -0.64 (0.27), residues: 464 *********************** 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 94 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.624 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 outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.5788 time to fit residues: 73.6788 Evaluate side-chains 76 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2088 time to fit residues: 2.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** A 588 ASN B 483 HIS B 494 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 10948 Z= 0.295 Angle : 0.672 7.237 14920 Z= 0.339 Chirality : 0.037 0.263 1716 Planarity : 0.005 0.041 1854 Dihedral : 5.258 20.472 1338 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.48 % 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: 0.07 (0.23), residues: 1212 helix: 0.45 (0.18), residues: 736 sheet: 1.29 (1.11), residues: 20 loop : -0.51 (0.29), residues: 456 *********************** 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 86 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.645 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 outliers start: 5 outliers final: 4 residues processed: 84 average time/residue: 0.6328 time to fit residues: 71.3225 Evaluate side-chains 74 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2219 time to fit residues: 3.6564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 10948 Z= 0.230 Angle : 0.626 7.373 14920 Z= 0.311 Chirality : 0.036 0.224 1716 Planarity : 0.004 0.073 1854 Dihedral : 5.041 19.445 1338 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.38 % 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: 0.42 (0.24), residues: 1212 helix: 0.71 (0.18), residues: 738 sheet: 1.50 (1.17), residues: 20 loop : -0.34 (0.30), residues: 454 *********************** 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 80 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 1.691 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 outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.5314 time to fit residues: 59.4006 Evaluate side-chains 75 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2215 time to fit residues: 3.7060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 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** A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 10948 Z= 0.321 Angle : 0.651 7.612 14920 Z= 0.328 Chirality : 0.037 0.220 1716 Planarity : 0.004 0.038 1854 Dihedral : 5.023 18.785 1338 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.38 % 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: 0.41 (0.24), residues: 1212 helix: 0.75 (0.19), residues: 734 sheet: 1.62 (1.19), residues: 20 loop : -0.44 (0.30), residues: 458 *********************** 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 78 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 2.722 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 outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.5786 time to fit residues: 61.0334 Evaluate side-chains 73 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2252 time to fit residues: 2.9414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 28 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7972 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10948 Z= 0.225 Angle : 0.603 7.553 14920 Z= 0.299 Chirality : 0.035 0.210 1716 Planarity : 0.004 0.035 1854 Dihedral : 4.892 18.484 1338 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.48 % 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: 0.67 (0.24), residues: 1212 helix: 0.96 (0.19), residues: 734 sheet: 1.28 (1.17), residues: 20 loop : -0.30 (0.31), residues: 458 *********************** 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 79 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 1.798 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 outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.5358 time to fit residues: 58.4516 Evaluate side-chains 73 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.604 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4833 time to fit residues: 4.6428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10948 Z= 0.201 Angle : 0.580 7.531 14920 Z= 0.288 Chirality : 0.034 0.214 1716 Planarity : 0.004 0.033 1854 Dihedral : 4.775 18.140 1338 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.76 % 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: 0.90 (0.24), residues: 1212 helix: 1.15 (0.19), residues: 736 sheet: 1.05 (1.18), residues: 20 loop : -0.21 (0.31), residues: 456 *********************** 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 81 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 1.494 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 outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.5158 time to fit residues: 59.9312 Evaluate side-chains 73 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.659 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2807 time to fit residues: 4.4619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 105 optimal weight: 0.0670 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10948 Z= 0.207 Angle : 0.577 7.519 14920 Z= 0.287 Chirality : 0.034 0.206 1716 Planarity : 0.004 0.031 1854 Dihedral : 4.698 18.315 1338 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.38 % 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: 1.24 (0.19), residues: 736 sheet: 1.02 (1.20), residues: 20 loop : -0.21 (0.31), residues: 456 *********************** 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 75 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 1.731 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 outliers start: 4 outliers final: 1 residues processed: 74 average time/residue: 0.4955 time to fit residues: 53.5567 Evaluate side-chains 70 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.625 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2182 time to fit residues: 2.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10948 Z= 0.214 Angle : 0.576 7.513 14920 Z= 0.286 Chirality : 0.034 0.197 1716 Planarity : 0.004 0.031 1854 Dihedral : 4.648 18.179 1338 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.48 % 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: 1.02 (0.24), residues: 1212 helix: 1.27 (0.19), residues: 738 sheet: 0.88 (1.21), residues: 20 loop : -0.20 (0.30), residues: 454 *********************** 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 77 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.687 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 outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 0.5364 time to fit residues: 56.6381 Evaluate side-chains 76 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.618 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2269 time to fit residues: 3.7064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3893 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= 0.201 Angle : 0.577 9.797 14920 Z= 0.285 Chirality : 0.034 0.194 1716 Planarity : 0.004 0.030 1854 Dihedral : 4.614 18.171 1338 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.10 % 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: 1.10 (0.24), residues: 1212 helix: 1.33 (0.19), residues: 738 sheet: 0.79 (1.22), residues: 20 loop : -0.17 (0.30), residues: 454 ********************** 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 76 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 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 outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.5256 time to fit residues: 56.2847 Evaluate side-chains 73 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.568 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2169 time to fit residues: 2.5855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.0980 chunk 14 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.092283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078337 restraints weight = 78856.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081510 restraints weight = 33908.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083613 restraints weight = 19176.252| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 10948 Z= 0.147 Angle : 0.541 8.026 14920 Z= 0.266 Chirality : 0.033 0.184 1716 Planarity : 0.003 0.025 1854 Dihedral : 4.432 17.672 1338 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.29 % 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: 1.38 (0.25), residues: 1212 helix: 1.55 (0.19), residues: 750 sheet: 0.54 (1.25), residues: 20 loop : -0.06 (0.31), residues: 442 =============================================================================== Job complete usr+sys time: 3611.40 seconds wall clock time: 65 minutes 25.15 seconds (3925.15 seconds total)