Starting phenix.real_space_refine on Fri Feb 16 08:07:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/02_2024/6vxp_21447.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/02_2024/6vxp_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_21447/02_2024/6vxp_21447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/02_2024/6vxp_21447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/02_2024/6vxp_21447.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/02_2024/6vxp_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-dev-5238/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: 8.19, per 1000 atoms: 0.55 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: 5.97 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: 1.65 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: 4.74 Time building geometry restraints manager: 6.43 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: 0.710 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: 4.420 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 41.890 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.510 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 397 HIS 0.003 0.001 HIS D 439 PHE 0.011 0.002 PHE G 239 TYR 0.010 0.001 TYR G 441 ARG 0.003 0.001 ARG C 444 *********************** 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 : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ASP cc_start: 0.7648 (t0) cc_final: 0.7422 (t0) REVERT: D 410 ASP cc_start: 0.7530 (t0) cc_final: 0.7317 (t0) REVERT: F 410 ASP cc_start: 0.7378 (t0) cc_final: 0.7130 (t0) REVERT: G 410 ASP cc_start: 0.7357 (t0) cc_final: 0.7113 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2916 time to fit residues: 111.3927 Evaluate side-chains 149 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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: 0.8004 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15050 Z= 0.154 Angle : 0.532 11.546 20335 Z= 0.264 Chirality : 0.038 0.141 2443 Planarity : 0.004 0.036 2520 Dihedral : 3.570 14.332 2030 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.22 % Allowed : 13.30 % Favored : 83.49 % 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: 1.68 (0.16), residues: 1099 sheet: -2.04 (0.25), residues: 315 loop : -2.75 (0.21), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 253 HIS 0.002 0.001 HIS D 484 PHE 0.021 0.001 PHE B 222 TYR 0.015 0.002 TYR D 256 ARG 0.003 0.000 ARG A 342 *********************** 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 220 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 1.838 Fit side-chains REVERT: B 219 PHE cc_start: 0.8323 (t80) cc_final: 0.8083 (t80) REVERT: E 228 MET cc_start: 0.1153 (ttm) cc_final: 0.0777 (ttt) outliers start: 52 outliers final: 31 residues processed: 189 average time/residue: 0.1916 time to fit residues: 59.7557 Evaluate side-chains 179 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 292 PHE Chi-restraints excluded: chain G residue 310 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 chunk 185 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.3172 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= 0.200 Angle : 0.520 12.099 20335 Z= 0.252 Chirality : 0.038 0.136 2443 Planarity : 0.003 0.034 2520 Dihedral : 3.206 10.752 2030 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.04 % Allowed : 15.71 % Favored : 82.25 % 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: 0.86 (0.20), residues: 1897 helix: 2.47 (0.16), residues: 1134 sheet: -2.01 (0.24), residues: 315 loop : -2.57 (0.23), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 206 HIS 0.002 0.001 HIS A 484 PHE 0.024 0.001 PHE E 222 TYR 0.016 0.002 TYR F 467 ARG 0.002 0.000 ARG F 265 *********************** 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 176 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.716 Fit side-chains REVERT: A 215 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: B 215 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: B 266 MET cc_start: 0.7350 (mmp) cc_final: 0.7142 (mmp) REVERT: C 215 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: C 413 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7410 (mtt) REVERT: D 215 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: E 215 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5868 (m-80) REVERT: F 215 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5978 (m-80) REVERT: G 215 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6029 (m-80) outliers start: 33 outliers final: 15 residues processed: 154 average time/residue: 0.1978 time to fit residues: 50.1544 Evaluate side-chains 160 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8147 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15050 Z= 0.251 Angle : 0.550 9.544 20335 Z= 0.266 Chirality : 0.038 0.141 2443 Planarity : 0.003 0.035 2520 Dihedral : 3.301 13.119 2030 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.03 % Allowed : 16.45 % Favored : 80.52 % 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: 1.48 (0.20), residues: 1897 helix: 2.89 (0.16), residues: 1127 sheet: -1.40 (0.27), residues: 301 loop : -2.34 (0.23), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 253 HIS 0.004 0.001 HIS C 484 PHE 0.019 0.001 PHE E 222 TYR 0.013 0.001 TYR C 467 ARG 0.002 0.000 ARG C 460 *********************** 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 177 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 1.803 Fit side-chains REVERT: A 215 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: B 215 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.5863 (m-80) REVERT: C 215 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: D 215 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: E 215 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: E 346 MET cc_start: 0.7872 (tpp) cc_final: 0.7244 (tpp) REVERT: F 215 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5884 (m-80) REVERT: G 215 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5846 (m-80) outliers start: 49 outliers final: 24 residues processed: 156 average time/residue: 0.2042 time to fit residues: 53.8254 Evaluate side-chains 153 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 310 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 0.0170 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 93 optimal weight: 0.2980 chunk 163 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.6622 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15050 Z= 0.185 Angle : 0.512 8.726 20335 Z= 0.244 Chirality : 0.038 0.128 2443 Planarity : 0.003 0.033 2520 Dihedral : 3.140 13.788 2030 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.60 % Allowed : 16.51 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1897 helix: 3.43 (0.15), residues: 1085 sheet: -0.85 (0.29), residues: 315 loop : -1.82 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 397 HIS 0.003 0.001 HIS B 484 PHE 0.022 0.001 PHE E 222 TYR 0.009 0.001 TYR D 256 ARG 0.001 0.000 ARG A 342 *********************** 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 174 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.825 Fit side-chains REVERT: A 215 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: B 215 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: C 215 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.5906 (m-80) REVERT: D 215 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.5994 (m-80) REVERT: E 215 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: E 228 MET cc_start: 0.0837 (ttm) cc_final: 0.0536 (ttt) REVERT: F 215 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.5882 (m-80) REVERT: G 215 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5814 (m-80) outliers start: 42 outliers final: 19 residues processed: 159 average time/residue: 0.1981 time to fit residues: 51.9284 Evaluate side-chains 149 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 7.9990 chunk 164 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15050 Z= 0.150 Angle : 0.503 8.168 20335 Z= 0.238 Chirality : 0.038 0.151 2443 Planarity : 0.003 0.031 2520 Dihedral : 3.076 13.967 2030 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.23 % Allowed : 17.01 % Favored : 80.77 % 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: 3.49 (0.15), residues: 1092 sheet: -0.86 (0.28), residues: 350 loop : -1.54 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 397 HIS 0.002 0.001 HIS C 484 PHE 0.027 0.001 PHE B 222 TYR 0.009 0.001 TYR D 256 ARG 0.001 0.000 ARG A 342 *********************** 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 168 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.889 Fit side-chains REVERT: A 215 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: B 215 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.5910 (m-80) REVERT: C 215 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5946 (m-80) REVERT: D 215 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5961 (m-80) REVERT: E 215 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: E 228 MET cc_start: 0.0889 (ttm) cc_final: 0.0595 (ttt) REVERT: E 413 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7586 (mtt) REVERT: F 215 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: G 215 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.5941 (m-80) outliers start: 36 outliers final: 19 residues processed: 150 average time/residue: 0.2066 time to fit residues: 50.7258 Evaluate side-chains 151 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 182 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15050 Z= 0.153 Angle : 0.509 9.650 20335 Z= 0.239 Chirality : 0.038 0.247 2443 Planarity : 0.003 0.028 2520 Dihedral : 3.076 17.503 2030 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.04 % Allowed : 17.50 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.20), residues: 1897 helix: 3.57 (0.15), residues: 1092 sheet: -0.67 (0.29), residues: 350 loop : -1.49 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP F 397 HIS 0.002 0.001 HIS C 484 PHE 0.037 0.001 PHE B 222 TYR 0.010 0.001 TYR C 467 ARG 0.002 0.000 ARG D 460 *********************** 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 158 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: B 215 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: C 215 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.5896 (m-80) REVERT: D 215 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: E 215 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: E 228 MET cc_start: 0.0899 (ttm) cc_final: 0.0624 (ttt) REVERT: E 413 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7571 (mtt) REVERT: F 215 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.5953 (m-80) REVERT: G 215 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.5918 (m-80) outliers start: 33 outliers final: 19 residues processed: 139 average time/residue: 0.2053 time to fit residues: 46.8274 Evaluate side-chains 150 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 30.0000 chunk 54 optimal weight: 40.0000 chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15050 Z= 0.192 Angle : 0.532 9.157 20335 Z= 0.249 Chirality : 0.039 0.295 2443 Planarity : 0.003 0.030 2520 Dihedral : 3.149 22.040 2030 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.98 % Allowed : 17.44 % Favored : 80.58 % 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: 2.56 (0.20), residues: 1897 helix: 3.59 (0.15), residues: 1092 sheet: -0.56 (0.29), residues: 350 loop : -1.41 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 253 HIS 0.003 0.001 HIS B 484 PHE 0.024 0.001 PHE E 222 TYR 0.010 0.001 TYR C 467 ARG 0.001 0.000 ARG B 460 *********************** 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 155 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 2.040 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6181 (m-80) REVERT: B 215 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.5913 (m-80) REVERT: C 215 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: D 215 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6102 (m-80) REVERT: E 215 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.5801 (m-80) REVERT: E 228 MET cc_start: 0.0970 (ttm) cc_final: 0.0673 (ttt) REVERT: F 215 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: F 228 MET cc_start: 0.4258 (ttm) cc_final: 0.3504 (mtt) REVERT: G 215 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5897 (m-80) outliers start: 32 outliers final: 21 residues processed: 137 average time/residue: 0.2084 time to fit residues: 46.7370 Evaluate side-chains 149 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU 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: 9.9990 chunk 169 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 73 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 179 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4708 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= 0.142 Angle : 0.529 9.787 20335 Z= 0.245 Chirality : 0.039 0.289 2443 Planarity : 0.003 0.028 2520 Dihedral : 3.146 19.730 2030 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 17.81 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.20), residues: 1897 helix: 3.61 (0.15), residues: 1092 sheet: -0.49 (0.30), residues: 350 loop : -1.32 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 397 HIS 0.004 0.001 HIS B 484 PHE 0.025 0.001 PHE E 222 TYR 0.009 0.001 TYR C 467 ARG 0.001 0.000 ARG A 342 *********************** 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 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: C 215 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.5779 (m-80) REVERT: E 215 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.5824 (m-80) REVERT: E 228 MET cc_start: 0.0966 (ttm) cc_final: 0.0688 (ttt) REVERT: F 215 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: F 228 MET cc_start: 0.4263 (ttm) cc_final: 0.3515 (mtt) outliers start: 29 outliers final: 20 residues processed: 137 average time/residue: 0.2032 time to fit residues: 45.8008 Evaluate side-chains 146 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 0.3980 chunk 188 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 471 GLN G 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4831 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= 0.150 Angle : 0.549 10.266 20335 Z= 0.252 Chirality : 0.040 0.326 2443 Planarity : 0.003 0.026 2520 Dihedral : 3.158 20.694 2030 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.67 % Allowed : 17.87 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.20), residues: 1897 helix: 3.62 (0.15), residues: 1092 sheet: -0.43 (0.30), residues: 350 loop : -1.31 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 397 HIS 0.005 0.001 HIS C 484 PHE 0.029 0.001 PHE G 222 TYR 0.008 0.001 TYR B 256 ARG 0.001 0.000 ARG C 460 ********************** 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 152 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: C 215 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5911 (m-80) REVERT: D 215 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: E 215 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5809 (m-80) REVERT: E 228 MET cc_start: 0.0976 (ttm) cc_final: 0.0687 (ttt) REVERT: F 215 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6029 (m-80) REVERT: F 228 MET cc_start: 0.4283 (ttm) cc_final: 0.3522 (mtt) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 0.2035 time to fit residues: 45.3428 Evaluate side-chains 146 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN E 471 GLN F 471 GLN G 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052775 restraints weight = 52234.549| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.79 r_work: 0.2686 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 15050 Z= 0.460 Angle : 0.702 10.325 20335 Z= 0.341 Chirality : 0.044 0.328 2443 Planarity : 0.004 0.034 2520 Dihedral : 3.681 22.603 2030 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 17.63 % Favored : 80.58 % 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: 2.53 (0.20), residues: 1897 helix: 3.47 (0.15), residues: 1092 sheet: -0.60 (0.29), residues: 350 loop : -1.10 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 253 HIS 0.012 0.004 HIS F 484 PHE 0.028 0.002 PHE G 222 TYR 0.014 0.002 TYR C 467 ARG 0.002 0.000 ARG A 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.63 seconds wall clock time: 48 minutes 2.82 seconds (2882.82 seconds total)