Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 15:22:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/10_2023/7jsk_22457_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/10_2023/7jsk_22457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/10_2023/7jsk_22457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/10_2023/7jsk_22457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/10_2023/7jsk_22457_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/10_2023/7jsk_22457_neut_trim_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 64 5.16 5 Na 4 4.78 5 C 4920 2.51 5 N 1152 2.21 5 O 1232 1.98 5 H 7664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 15036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7489 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "B" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7489 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' NA': 2, 'CIT': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' NA': 2, 'CIT': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.59, per 1000 atoms: 0.44 Number of scatterers: 15036 At special positions: 0 Unit cell: (76.504, 103.752, 84.888, 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) S 64 16.00 Na 4 11.00 O 1232 8.00 N 1152 7.00 C 4920 6.00 H 7664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 562 " " NAG B 601 " - " ASN B 562 " Time building additional restraints: 13.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Proline residue: A 21 - end of helix removed outlier: 4.395A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.760A pdb=" N MET A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 76 through 82 removed outlier: 4.375A pdb=" N GLN A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 142 through 157 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.924A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 250 through 275 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.740A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.520A pdb=" N PHE A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 332 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A 333 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 4.070A pdb=" N PHE A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 442 removed outlier: 3.774A pdb=" N ALA A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 445 through 461 removed outlier: 4.145A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Proline residue: A 474 - end of helix Processing helix chain 'A' and resid 487 through 498 removed outlier: 4.789A pdb=" N LEU A 492 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.934A pdb=" N TYR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 removed outlier: 4.302A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'B' and resid 16 through 28 Proline residue: B 21 - end of helix removed outlier: 4.395A pdb=" N LEU B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Proline residue: B 26 - end of helix Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.762A pdb=" N MET B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 76 through 82 removed outlier: 4.376A pdb=" N GLN B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 Processing helix chain 'B' and resid 106 through 117 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 142 through 157 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.924A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 250 through 275 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.740A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.520A pdb=" N PHE B 331 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 332 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 333 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 4.070A pdb=" N PHE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 439 through 442 removed outlier: 3.775A pdb=" N ALA B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 445 through 461 removed outlier: 4.144A pdb=" N GLU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Proline residue: B 474 - end of helix Processing helix chain 'B' and resid 487 through 498 removed outlier: 4.788A pdb=" N LEU B 492 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.934A pdb=" N TYR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 removed outlier: 4.301A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 400 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 13.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7644 1.03 - 1.22: 24 1.22 - 1.42: 3006 1.42 - 1.61: 4440 1.61 - 1.81: 108 Bond restraints: 15222 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.593 -0.061 2.00e-02 2.50e+03 9.20e+00 bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.593 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.391 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C7 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.346 1.390 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" CA ALA A 119 " pdb=" CB ALA A 119 " ideal model delta sigma weight residual 1.525 1.495 0.030 1.47e-02 4.63e+03 4.04e+00 ... (remaining 15217 not shown) Histogram of bond angle deviations from ideal: 71.28 - 84.75: 142 84.75 - 98.22: 13 98.22 - 111.69: 17684 111.69 - 125.16: 9426 125.16 - 138.62: 447 Bond angle restraints: 27712 Sorted by residual: angle pdb=" N VAL B 263 " pdb=" CA VAL B 263 " pdb=" HA VAL B 263 " ideal model delta sigma weight residual 110.00 71.28 38.72 3.00e+00 1.11e-01 1.67e+02 angle pdb=" N VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 110.00 71.43 38.57 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C PHE A 14 " pdb=" CA PHE A 14 " pdb=" HA PHE A 14 " ideal model delta sigma weight residual 109.00 72.35 36.65 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C PHE B 14 " pdb=" CA PHE B 14 " pdb=" HA PHE B 14 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" HA SER A 13 " ideal model delta sigma weight residual 110.00 73.55 36.45 3.00e+00 1.11e-01 1.48e+02 ... (remaining 27707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 5170 15.47 - 30.94: 696 30.94 - 46.42: 140 46.42 - 61.89: 64 61.89 - 77.36: 4 Dihedral angle restraints: 6074 sinusoidal: 2770 harmonic: 3304 Sorted by residual: dihedral pdb=" CA THR A 225 " pdb=" C THR A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR B 225 " pdb=" C THR B 225 " pdb=" N GLY B 226 " pdb=" CA GLY B 226 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA TYR A 353 " pdb=" C TYR A 353 " pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 6071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 1216 0.341 - 0.683: 8 0.683 - 1.024: 6 1.024 - 1.365: 2 1.365 - 1.707: 16 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CG LEU A 440 " pdb=" CB LEU A 440 " pdb=" CD1 LEU A 440 " pdb=" CD2 LEU A 440 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CG LEU B 440 " pdb=" CB LEU B 440 " pdb=" CD1 LEU B 440 " pdb=" CD2 LEU B 440 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.24e+01 chirality pdb=" CG LEU A 111 " pdb=" CB LEU A 111 " pdb=" CD1 LEU A 111 " pdb=" CD2 LEU A 111 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 ... (remaining 1245 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 310 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 311 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 311 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 310 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 311 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 406 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO B 407 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " 0.029 5.00e-02 4.00e+02 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 286 2.07 - 2.70: 25312 2.70 - 3.34: 45290 3.34 - 3.97: 55264 3.97 - 4.60: 89976 Nonbonded interactions: 216128 Sorted by model distance: nonbonded pdb=" OD1 ASN A 141 " pdb="NA NA A 603 " model vdw 1.439 2.350 nonbonded pdb=" OD1 ASN B 141 " pdb="NA NA B 603 " model vdw 1.442 2.350 nonbonded pdb=" O MET B 31 " pdb=" H ALA B 33 " model vdw 1.611 1.850 nonbonded pdb=" O LYS A 120 " pdb=" H LEU A 124 " model vdw 1.615 1.850 nonbonded pdb=" O MET A 31 " pdb=" H ALA A 33 " model vdw 1.618 1.850 ... (remaining 216123 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.200 Extract box with map and model: 4.240 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 50.110 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.011 0.063 7558 Z= 0.724 Angle : 1.157 16.678 10308 Z= 0.576 Chirality : 0.205 1.707 1248 Planarity : 0.006 0.055 1236 Dihedral : 14.686 77.359 2658 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % Rotamer: Outliers : 4.74 % Allowed : 10.10 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.29), residues: 916 helix: 0.45 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.89 (0.42), residues: 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.041 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: 38 outliers final: 13 residues processed: 208 average time/residue: 0.4527 time to fit residues: 124.7118 Evaluate side-chains 140 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.153 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.1955 time to fit residues: 5.8023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 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 157 GLN A 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7558 Z= 0.212 Angle : 0.948 15.857 10308 Z= 0.448 Chirality : 0.212 1.772 1248 Planarity : 0.006 0.048 1236 Dihedral : 6.043 46.731 982 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.42 % Favored : 92.36 % Rotamer: Outliers : 3.12 % Allowed : 14.84 % Favored : 82.04 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.25 (0.30), residues: 916 helix: 0.85 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.97 (0.42), residues: 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 1.128 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 outliers start: 25 outliers final: 12 residues processed: 171 average time/residue: 0.3638 time to fit residues: 90.4338 Evaluate side-chains 143 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.119 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 12 average time/residue: 0.1894 time to fit residues: 5.4704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7558 Z= 0.252 Angle : 0.941 15.777 10308 Z= 0.442 Chirality : 0.210 1.770 1248 Planarity : 0.005 0.044 1236 Dihedral : 5.622 51.516 982 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.30 % Favored : 91.48 % Rotamer: Outliers : 1.37 % Allowed : 16.71 % Favored : 81.92 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 916 helix: 0.93 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -2.81 (0.41), residues: 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.124 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 outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.3546 time to fit residues: 67.5342 Evaluate side-chains 125 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.251 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 8 average time/residue: 0.1966 time to fit residues: 4.2626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.004 0.039 7558 Z= 0.254 Angle : 0.933 15.651 10308 Z= 0.439 Chirality : 0.210 1.756 1248 Planarity : 0.005 0.040 1236 Dihedral : 5.613 56.560 982 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.41 % Favored : 91.38 % Rotamer: Outliers : 1.87 % Allowed : 17.96 % Favored : 80.17 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.30), residues: 916 helix: 1.02 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -2.88 (0.40), residues: 266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.091 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 outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.3925 time to fit residues: 75.6637 Evaluate side-chains 123 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.143 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 10 average time/residue: 0.1927 time to fit residues: 4.9453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7558 Z= 0.273 Angle : 0.940 15.692 10308 Z= 0.443 Chirality : 0.211 1.758 1248 Planarity : 0.005 0.045 1236 Dihedral : 5.638 58.294 982 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.73 % Favored : 91.05 % Rotamer: Outliers : 1.50 % Allowed : 19.33 % Favored : 79.18 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.30), residues: 916 helix: 0.97 (0.21), residues: 662 sheet: None (None), residues: 0 loop : -3.20 (0.39), residues: 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.272 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 outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 0.3735 time to fit residues: 70.8818 Evaluate side-chains 117 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.278 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.1896 time to fit residues: 3.4835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7558 Z= 0.235 Angle : 0.925 15.692 10308 Z= 0.434 Chirality : 0.210 1.768 1248 Planarity : 0.005 0.050 1236 Dihedral : 5.493 54.138 982 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.30 % Favored : 91.48 % Rotamer: Outliers : 1.50 % Allowed : 19.45 % Favored : 79.05 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.30), residues: 916 helix: 1.21 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -2.88 (0.40), residues: 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.084 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 outliers start: 12 outliers final: 7 residues processed: 134 average time/residue: 0.3766 time to fit residues: 70.6155 Evaluate side-chains 128 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.083 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.1741 time to fit residues: 3.5777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 65 optimal weight: 0.2980 chunk 74 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7558 Z= 0.195 Angle : 0.910 15.639 10308 Z= 0.422 Chirality : 0.210 1.770 1248 Planarity : 0.005 0.057 1236 Dihedral : 5.186 50.744 982 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.97 % Favored : 91.81 % Rotamer: Outliers : 1.37 % Allowed : 19.58 % Favored : 79.05 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.31), residues: 916 helix: 1.44 (0.22), residues: 660 sheet: None (None), residues: 0 loop : -2.88 (0.41), residues: 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 144 average time/residue: 0.3516 time to fit residues: 72.6298 Evaluate side-chains 128 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.095 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.1872 time to fit residues: 4.0189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7558 Z= 0.213 Angle : 0.918 15.701 10308 Z= 0.427 Chirality : 0.210 1.783 1248 Planarity : 0.005 0.039 1236 Dihedral : 5.137 50.720 982 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.08 % Favored : 91.70 % Rotamer: Outliers : 0.87 % Allowed : 20.45 % Favored : 78.68 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 916 helix: 1.49 (0.22), residues: 664 sheet: None (None), residues: 0 loop : -2.85 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 128 average time/residue: 0.3285 time to fit residues: 61.4627 Evaluate side-chains 128 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.081 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.1598 time to fit residues: 2.2173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.0170 chunk 53 optimal weight: 0.9980 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7558 Z= 0.216 Angle : 0.921 15.758 10308 Z= 0.428 Chirality : 0.210 1.787 1248 Planarity : 0.005 0.049 1236 Dihedral : 5.108 51.068 982 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.19 % Favored : 91.59 % Rotamer: Outliers : 0.87 % Allowed : 20.07 % Favored : 79.05 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.31), residues: 916 helix: 1.61 (0.22), residues: 656 sheet: None (None), residues: 0 loop : -2.84 (0.40), residues: 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 128 average time/residue: 0.3448 time to fit residues: 64.5913 Evaluate side-chains 125 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.158 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.1691 time to fit residues: 2.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7558 Z= 0.227 Angle : 0.924 15.743 10308 Z= 0.431 Chirality : 0.210 1.791 1248 Planarity : 0.005 0.069 1236 Dihedral : 5.089 51.502 982 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.30 % Favored : 91.48 % Rotamer: Outliers : 0.62 % Allowed : 20.57 % Favored : 78.80 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.31), residues: 916 helix: 1.57 (0.22), residues: 668 sheet: None (None), residues: 0 loop : -2.84 (0.42), residues: 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.142 Fit side-chains 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: 128 average time/residue: 0.3358 time to fit residues: 63.0721 Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.214 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.1704 time to fit residues: 2.8385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113712 restraints weight = 33784.640| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.02 r_work: 0.3489 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7558 Z= 0.214 Angle : 0.924 15.761 10308 Z= 0.430 Chirality : 0.210 1.789 1248 Planarity : 0.004 0.036 1236 Dihedral : 5.034 51.697 982 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.19 % Favored : 91.59 % Rotamer: Outliers : 0.75 % Allowed : 20.70 % Favored : 78.55 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.31), residues: 916 helix: 1.62 (0.22), residues: 668 sheet: None (None), residues: 0 loop : -2.79 (0.42), residues: 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3743.02 seconds wall clock time: 67 minutes 10.03 seconds (4030.03 seconds total)