Starting phenix.real_space_refine on Thu Nov 16 08:13:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/11_2023/6vxp_21447.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/11_2023/6vxp_21447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/11_2023/6vxp_21447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/11_2023/6vxp_21447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/11_2023/6vxp_21447.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/11_2023/6vxp_21447.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9534 2.51 5 N 2485 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "E ARG 265": "NH1" <-> "NH2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F ARG 426": "NH1" <-> "NH2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "G ARG 265": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G GLU 446": "OE1" <-> "OE2" Residue "G ARG 460": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 14819 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "B" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "C" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "D" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "E" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "F" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "G" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Time building chain proxies: 8.47, per 1000 atoms: 0.57 Number of scatterers: 14819 At special positions: 0 Unit cell: (101.2, 102.3, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2716 8.00 N 2485 7.00 C 9534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 3.1 seconds 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 58.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 204 through 229 Proline residue: A 212 - end of helix removed outlier: 3.574A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 266 Processing helix chain 'A' and resid 277 through 304 Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 325 through 341 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.551A pdb=" N TYR A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 229 Proline residue: B 212 - end of helix removed outlier: 3.574A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 266 Processing helix chain 'B' and resid 277 through 304 Processing helix chain 'B' and resid 306 through 325 Processing helix chain 'B' and resid 325 through 341 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 229 Proline residue: C 212 - end of helix removed outlier: 3.574A pdb=" N ILE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 266 Processing helix chain 'C' and resid 277 through 304 Processing helix chain 'C' and resid 306 through 325 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 229 Proline residue: D 212 - end of helix removed outlier: 3.574A pdb=" N ILE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 266 Processing helix chain 'D' and resid 277 through 304 Processing helix chain 'D' and resid 306 through 325 Processing helix chain 'D' and resid 325 through 341 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 413 through 427 Processing helix chain 'D' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 229 Proline residue: E 212 - end of helix removed outlier: 3.574A pdb=" N ILE E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 266 Processing helix chain 'E' and resid 277 through 304 Processing helix chain 'E' and resid 306 through 325 Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 413 through 427 Processing helix chain 'E' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS E 484 " --> pdb=" O ILE E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 229 Proline residue: F 212 - end of helix removed outlier: 3.574A pdb=" N ILE F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 266 Processing helix chain 'F' and resid 277 through 304 Processing helix chain 'F' and resid 306 through 325 Processing helix chain 'F' and resid 325 through 341 Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS F 484 " --> pdb=" O ILE F 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 229 Proline residue: G 212 - end of helix removed outlier: 3.574A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 229 " --> pdb=" O ILE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 266 Processing helix chain 'G' and resid 277 through 304 Processing helix chain 'G' and resid 306 through 325 Processing helix chain 'G' and resid 325 through 341 Processing helix chain 'G' and resid 382 through 384 No H-bonds generated for 'chain 'G' and resid 382 through 384' Processing helix chain 'G' and resid 410 through 412 No H-bonds generated for 'chain 'G' and resid 410 through 412' Processing helix chain 'G' and resid 413 through 427 Processing helix chain 'G' and resid 463 through 484 removed outlier: 3.551A pdb=" N TYR G 467 " --> pdb=" O LYS G 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.007A pdb=" N VAL A 359 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 370 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL G 359 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 370 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL F 359 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 370 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL E 359 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU E 370 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL D 359 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU D 370 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL C 359 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 370 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL B 359 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 370 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU A 451 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 445 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 487 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU B 451 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 445 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 487 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU C 451 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL C 445 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 487 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 439 through 446 removed outlier: 6.838A pdb=" N GLU D 451 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL D 445 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 487 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 439 through 446 removed outlier: 6.838A pdb=" N GLU E 451 " --> pdb=" O SER E 443 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL E 445 " --> pdb=" O PHE E 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 487 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU F 451 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL F 445 " --> pdb=" O PHE F 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER F 487 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU G 451 " --> pdb=" O SER G 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL G 445 " --> pdb=" O PHE G 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE G 449 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER G 487 " --> pdb=" O GLN G 407 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 3150 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: 4.70 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4351 1.33 - 1.45: 2037 1.45 - 1.57: 8502 1.57 - 1.69: 13 1.69 - 1.80: 147 Bond restraints: 15050 Sorted by residual: bond pdb=" CA MET E 266 " pdb=" C MET E 266 " ideal model delta sigma weight residual 1.523 1.610 -0.088 1.41e-02 5.03e+03 3.88e+01 bond pdb=" CA MET F 266 " pdb=" C MET F 266 " ideal model delta sigma weight residual 1.523 1.610 -0.088 1.41e-02 5.03e+03 3.86e+01 bond pdb=" CA MET G 266 " pdb=" C MET G 266 " ideal model delta sigma weight residual 1.523 1.610 -0.087 1.41e-02 5.03e+03 3.83e+01 bond pdb=" CA MET C 266 " pdb=" C MET C 266 " ideal model delta sigma weight residual 1.523 1.610 -0.087 1.41e-02 5.03e+03 3.83e+01 bond pdb=" CA MET B 266 " pdb=" C MET B 266 " ideal model delta sigma weight residual 1.523 1.610 -0.087 1.41e-02 5.03e+03 3.83e+01 ... (remaining 15045 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.29: 340 105.29 - 112.48: 7933 112.48 - 119.66: 4879 119.66 - 126.84: 7028 126.84 - 134.02: 155 Bond angle restraints: 20335 Sorted by residual: angle pdb=" N VAL E 252 " pdb=" CA VAL E 252 " pdb=" C VAL E 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL A 252 " pdb=" CA VAL A 252 " pdb=" C VAL A 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL G 252 " pdb=" CA VAL G 252 " pdb=" C VAL G 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL D 252 " pdb=" CA VAL D 252 " pdb=" C VAL D 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL B 252 " pdb=" CA VAL B 252 " pdb=" C VAL B 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 ... (remaining 20330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.14: 8203 13.14 - 26.27: 638 26.27 - 39.41: 182 39.41 - 52.54: 35 52.54 - 65.68: 14 Dihedral angle restraints: 9072 sinusoidal: 3521 harmonic: 5551 Sorted by residual: dihedral pdb=" C MET G 266 " pdb=" N MET G 266 " pdb=" CA MET G 266 " pdb=" CB MET G 266 " ideal model delta harmonic sigma weight residual -122.60 -110.75 -11.85 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" C MET B 266 " pdb=" N MET B 266 " pdb=" CA MET B 266 " pdb=" CB MET B 266 " ideal model delta harmonic sigma weight residual -122.60 -110.76 -11.84 0 2.50e+00 1.60e-01 2.24e+01 dihedral pdb=" C MET F 266 " pdb=" N MET F 266 " pdb=" CA MET F 266 " pdb=" CB MET F 266 " ideal model delta harmonic sigma weight residual -122.60 -110.77 -11.83 0 2.50e+00 1.60e-01 2.24e+01 ... (remaining 9069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1954 0.067 - 0.133: 380 0.133 - 0.200: 57 0.200 - 0.266: 17 0.266 - 0.333: 35 Chirality restraints: 2443 Sorted by residual: chirality pdb=" CA SER E 250 " pdb=" N SER E 250 " pdb=" C SER E 250 " pdb=" CB SER E 250 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ARG F 265 " pdb=" N ARG F 265 " pdb=" C ARG F 265 " pdb=" CB ARG F 265 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER B 250 " pdb=" N SER B 250 " pdb=" C SER B 250 " pdb=" CB SER B 250 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2440 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 445 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C VAL E 445 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL E 445 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU E 446 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 445 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C VAL F 445 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL F 445 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU F 446 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 445 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C VAL C 445 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL C 445 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU C 446 " -0.013 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2689 2.76 - 3.30: 13748 3.30 - 3.83: 23156 3.83 - 4.37: 26985 4.37 - 4.90: 49381 Nonbonded interactions: 115959 Sorted by model distance: nonbonded pdb=" OG SER G 443 " pdb=" OE1 GLU G 451 " model vdw 2.226 2.440 nonbonded pdb=" OG SER B 443 " pdb=" OE1 GLU B 451 " model vdw 2.226 2.440 nonbonded pdb=" OG SER C 443 " pdb=" OE1 GLU C 451 " model vdw 2.227 2.440 nonbonded pdb=" OG SER E 443 " pdb=" OE1 GLU E 451 " model vdw 2.227 2.440 nonbonded pdb=" OG SER A 443 " pdb=" OE1 GLU A 451 " model vdw 2.227 2.440 ... (remaining 115954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.460 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 42.390 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 0.088 15050 Z= 0.511 Angle : 1.131 12.307 20335 Z= 0.792 Chirality : 0.067 0.333 2443 Planarity : 0.005 0.050 2520 Dihedral : 11.357 65.677 5474 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), residues: 1897 helix: -0.26 (0.15), residues: 1092 sheet: -2.63 (0.22), residues: 315 loop : -3.43 (0.20), residues: 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.743 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: 0 outliers final: 0 residues processed: 270 average time/residue: 0.3029 time to fit residues: 116.6542 Evaluate side-chains 149 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 171 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 261 ASN A 308 GLN A 331 ASN A 387 GLN B 261 ASN B 308 GLN B 331 ASN B 387 GLN C 261 ASN C 308 GLN C 331 ASN C 387 GLN D 261 ASN D 308 GLN D 331 ASN D 387 GLN E 261 ASN E 308 GLN E 331 ASN E 387 GLN F 261 ASN F 308 GLN F 331 ASN F 387 GLN G 308 GLN G 331 ASN G 387 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15050 Z= 0.157 Angle : 0.533 11.604 20335 Z= 0.264 Chirality : 0.038 0.141 2443 Planarity : 0.004 0.036 2520 Dihedral : 3.554 14.242 2030 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.28 % Allowed : 13.17 % Favored : 83.55 % 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: -0.08 (0.19), residues: 1897 helix: 1.67 (0.16), residues: 1099 sheet: -2.04 (0.25), residues: 315 loop : -2.73 (0.21), residues: 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 166 time to evaluate : 1.914 Fit side-chains outliers start: 53 outliers final: 30 residues processed: 188 average time/residue: 0.1993 time to fit residues: 61.7752 Evaluate side-chains 179 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.879 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1280 time to fit residues: 9.6367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 0.0670 chunk 185 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 428 ASN D 428 ASN E 428 ASN F 261 ASN F 428 ASN G 428 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15050 Z= 0.301 Angle : 0.580 12.258 20335 Z= 0.285 Chirality : 0.039 0.140 2443 Planarity : 0.004 0.037 2520 Dihedral : 3.429 11.071 2030 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 15.52 % Favored : 83.30 % 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: 0.88 (0.20), residues: 1897 helix: 2.50 (0.16), residues: 1127 sheet: -1.96 (0.25), residues: 301 loop : -2.57 (0.22), residues: 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.815 Fit side-chains outliers start: 19 outliers final: 3 residues processed: 142 average time/residue: 0.2392 time to fit residues: 55.7424 Evaluate side-chains 133 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1301 time to fit residues: 3.2402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15050 Z= 0.217 Angle : 0.519 9.045 20335 Z= 0.251 Chirality : 0.038 0.131 2443 Planarity : 0.003 0.034 2520 Dihedral : 3.248 10.870 2030 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.73 % Allowed : 16.76 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1897 helix: 2.88 (0.16), residues: 1127 sheet: -1.56 (0.26), residues: 315 loop : -2.47 (0.23), residues: 455 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.784 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 144 average time/residue: 0.2039 time to fit residues: 48.6885 Evaluate side-chains 141 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1308 time to fit residues: 6.0528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.6980 chunk 103 optimal weight: 0.0060 chunk 2 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 93 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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: 0.8079 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15050 Z= 0.117 Angle : 0.492 8.550 20335 Z= 0.233 Chirality : 0.037 0.122 2443 Planarity : 0.003 0.030 2520 Dihedral : 3.030 12.195 2030 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.36 % Allowed : 15.89 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1897 helix: 3.40 (0.15), residues: 1085 sheet: -1.00 (0.28), residues: 322 loop : -1.82 (0.24), residues: 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.880 Fit side-chains outliers start: 22 outliers final: 1 residues processed: 161 average time/residue: 0.2275 time to fit residues: 60.7833 Evaluate side-chains 136 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.782 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1708 time to fit residues: 2.8020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15050 Z= 0.192 Angle : 0.518 7.826 20335 Z= 0.246 Chirality : 0.038 0.150 2443 Planarity : 0.003 0.030 2520 Dihedral : 3.098 16.492 2030 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.24 % Allowed : 17.19 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.20), residues: 1897 helix: 3.53 (0.15), residues: 1092 sheet: -0.96 (0.28), residues: 357 loop : -1.53 (0.25), residues: 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.962 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 130 average time/residue: 0.2179 time to fit residues: 46.4751 Evaluate side-chains 135 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1281 time to fit residues: 4.7862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15050 Z= 0.228 Angle : 0.542 8.897 20335 Z= 0.257 Chirality : 0.038 0.222 2443 Planarity : 0.003 0.031 2520 Dihedral : 3.166 15.388 2030 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.49 % Allowed : 17.87 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.20), residues: 1897 helix: 3.55 (0.15), residues: 1092 sheet: -0.73 (0.29), residues: 350 loop : -1.45 (0.26), residues: 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.771 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 127 average time/residue: 0.2123 time to fit residues: 44.3679 Evaluate side-chains 128 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1325 time to fit residues: 3.4901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 108 optimal weight: 30.0000 chunk 54 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.8134 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15050 Z= 0.154 Angle : 0.517 10.021 20335 Z= 0.243 Chirality : 0.038 0.272 2443 Planarity : 0.003 0.028 2520 Dihedral : 3.191 22.583 2030 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.68 % Allowed : 18.24 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.20), residues: 1897 helix: 3.61 (0.15), residues: 1092 sheet: -0.60 (0.29), residues: 350 loop : -1.32 (0.26), residues: 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.750 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 128 average time/residue: 0.2134 time to fit residues: 44.9116 Evaluate side-chains 136 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1338 time to fit residues: 4.7083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.8980 chunk 159 optimal weight: 0.2980 chunk 169 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15050 Z= 0.141 Angle : 0.523 10.872 20335 Z= 0.244 Chirality : 0.039 0.264 2443 Planarity : 0.003 0.027 2520 Dihedral : 3.129 19.378 2030 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.19 % Allowed : 18.18 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.20), residues: 1897 helix: 3.62 (0.15), residues: 1092 sheet: -0.52 (0.30), residues: 350 loop : -1.26 (0.27), residues: 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.818 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.2130 time to fit residues: 46.1804 Evaluate side-chains 129 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1299 time to fit residues: 2.8187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN C 471 GLN D 471 GLN G 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15050 Z= 0.185 Angle : 0.554 10.273 20335 Z= 0.258 Chirality : 0.040 0.300 2443 Planarity : 0.003 0.027 2520 Dihedral : 3.224 23.364 2030 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 18.99 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.20), residues: 1897 helix: 3.65 (0.15), residues: 1092 sheet: -0.13 (0.32), residues: 315 loop : -1.31 (0.26), residues: 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.002 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2207 time to fit residues: 45.9440 Evaluate side-chains 125 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 154 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 40.0000 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN E 471 GLN F 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.073850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053686 restraints weight = 51874.946| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.76 r_work: 0.2704 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15050 Z= 0.369 Angle : 0.646 10.326 20335 Z= 0.312 Chirality : 0.043 0.329 2443 Planarity : 0.003 0.033 2520 Dihedral : 3.535 23.469 2030 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.80 % Allowed : 18.18 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.20), residues: 1897 helix: 3.54 (0.15), residues: 1092 sheet: -0.53 (0.29), residues: 350 loop : -1.03 (0.29), residues: 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.59 seconds wall clock time: 49 minutes 44.62 seconds (2984.62 seconds total)