Starting phenix.real_space_refine on Wed Feb 14 18:12:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch1_30368/02_2024/7ch1_30368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch1_30368/02_2024/7ch1_30368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch1_30368/02_2024/7ch1_30368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch1_30368/02_2024/7ch1_30368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch1_30368/02_2024/7ch1_30368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch1_30368/02_2024/7ch1_30368.pdb" } resolution = 2.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 66 5.16 5 Cl 4 4.86 5 Na 2 4.78 5 C 6502 2.51 5 N 1576 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 775": "OE1" <-> "OE2" Residue "B GLU 777": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9948 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 4933 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 28, 'TRANS': 611} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 4933 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 28, 'TRANS': 611} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Time building chain proxies: 5.56, per 1000 atoms: 0.56 Number of scatterers: 9948 At special positions: 0 Unit cell: (103.645, 118.919, 111.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 66 16.00 Na 2 11.00 O 1798 8.00 N 1576 7.00 C 6502 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 7 sheets defined 65.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.743A pdb=" N ASP A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 66 through 96 removed outlier: 6.185A pdb=" N ILE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix removed outlier: 3.971A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix removed outlier: 3.505A pdb=" N LEU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 109 through 118 removed outlier: 4.126A pdb=" N THR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.589A pdb=" N ASN A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 161 through 191 removed outlier: 3.543A pdb=" N HIS A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 219 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 248 through 251 removed outlier: 3.596A pdb=" N THR A 251 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 252 through 272 removed outlier: 3.544A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.606A pdb=" N VAL A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.505A pdb=" N TRP A 330 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 331 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 360 removed outlier: 3.509A pdb=" N SER A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.699A pdb=" N MET A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.751A pdb=" N SER A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 414 " --> pdb=" O CYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 441 removed outlier: 3.812A pdb=" N ASN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.644A pdb=" N TYR A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.701A pdb=" N ILE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 497 Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.713A pdb=" N ARG A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 Processing helix chain 'A' and resid 676 through 693 removed outlier: 3.949A pdb=" N ILE A 693 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 774 through 778 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.743A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 66 through 96 removed outlier: 6.185A pdb=" N ILE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Proline residue: B 73 - end of helix removed outlier: 3.971A pdb=" N ILE B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Proline residue: B 87 - end of helix removed outlier: 3.505A pdb=" N LEU B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 109 through 118 removed outlier: 4.126A pdb=" N THR B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 removed outlier: 3.589A pdb=" N ASN B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 161 through 191 removed outlier: 3.543A pdb=" N HIS B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 219 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 248 through 251 removed outlier: 3.596A pdb=" N THR B 251 " --> pdb=" O LEU B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 252 through 272 removed outlier: 3.544A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 299 removed outlier: 3.606A pdb=" N VAL B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.505A pdb=" N TRP B 330 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS B 331 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 360 removed outlier: 3.509A pdb=" N SER B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 381 removed outlier: 3.699A pdb=" N MET B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.751A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 414 " --> pdb=" O CYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 441 removed outlier: 3.812A pdb=" N ASN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 450 through 459 removed outlier: 3.644A pdb=" N TYR B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.701A pdb=" N ILE B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 497 Processing helix chain 'B' and resid 542 through 555 removed outlier: 3.713A pdb=" N ARG B 547 " --> pdb=" O SER B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 Processing helix chain 'B' and resid 676 through 693 removed outlier: 3.949A pdb=" N ILE B 693 " --> pdb=" O THR B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 713 Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 729 through 741 Processing helix chain 'B' and resid 774 through 778 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 504 removed outlier: 6.431A pdb=" N LYS A 530 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A 668 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 532 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE A 727 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 699 " --> pdb=" O PHE A 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA6, first strand: chain 'B' and resid 503 through 504 removed outlier: 6.431A pdb=" N LYS B 530 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP B 668 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 532 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE B 727 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 699 " --> pdb=" O PHE B 727 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 514 through 515 538 hydrogen bonds defined for protein. 1572 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: 3.13 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2970 1.34 - 1.46: 1798 1.46 - 1.57: 5220 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10096 Sorted by residual: bond pdb=" C LEU A 478 " pdb=" N PRO A 479 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.25e-02 6.40e+03 1.97e+01 bond pdb=" C LEU B 478 " pdb=" N PRO B 479 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.25e-02 6.40e+03 1.97e+01 bond pdb=" N PRO B 479 " pdb=" CD PRO B 479 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" C VAL A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 1.336 1.374 -0.038 1.20e-02 6.94e+03 1.02e+01 ... (remaining 10091 not shown) Histogram of bond angle deviations from ideal: 98.04 - 106.16: 276 106.16 - 114.28: 5940 114.28 - 122.40: 6332 122.40 - 130.52: 1096 130.52 - 138.64: 50 Bond angle restraints: 13694 Sorted by residual: angle pdb=" C LEU B 478 " pdb=" N PRO B 479 " pdb=" CA PRO B 479 " ideal model delta sigma weight residual 119.56 114.18 5.38 1.01e+00 9.80e-01 2.83e+01 angle pdb=" C LEU A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.56 114.18 5.38 1.01e+00 9.80e-01 2.83e+01 angle pdb=" N PHE B 475 " pdb=" CA PHE B 475 " pdb=" C PHE B 475 " ideal model delta sigma weight residual 112.68 118.33 -5.65 1.33e+00 5.65e-01 1.81e+01 angle pdb=" N PHE A 475 " pdb=" CA PHE A 475 " pdb=" C PHE A 475 " ideal model delta sigma weight residual 112.68 118.33 -5.65 1.33e+00 5.65e-01 1.81e+01 angle pdb=" C SER A 459 " pdb=" N LYS A 460 " pdb=" CA LYS A 460 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 ... (remaining 13689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5414 17.85 - 35.70: 376 35.70 - 53.55: 86 53.55 - 71.40: 66 71.40 - 89.26: 10 Dihedral angle restraints: 5952 sinusoidal: 2258 harmonic: 3694 Sorted by residual: dihedral pdb=" CA PHE A 282 " pdb=" C PHE A 282 " pdb=" N PRO A 283 " pdb=" CA PRO A 283 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE B 282 " pdb=" C PHE B 282 " pdb=" N PRO B 283 " pdb=" CA PRO B 283 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ARG B 281 " pdb=" C ARG B 281 " pdb=" N PHE B 282 " pdb=" CA PHE B 282 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 5949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1384 0.073 - 0.145: 210 0.145 - 0.218: 16 0.218 - 0.291: 0 0.291 - 0.363: 2 Chirality restraints: 1612 Sorted by residual: chirality pdb=" CB VAL A 292 " pdb=" CA VAL A 292 " pdb=" CG1 VAL A 292 " pdb=" CG2 VAL A 292 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB VAL B 292 " pdb=" CA VAL B 292 " pdb=" CG1 VAL B 292 " pdb=" CG2 VAL B 292 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE B 284 " pdb=" CA ILE B 284 " pdb=" CG1 ILE B 284 " pdb=" CG2 ILE B 284 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1609 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 248 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO B 249 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 248 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO A 249 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 249 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 249 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 303 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 304 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " -0.036 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1634 2.75 - 3.29: 8868 3.29 - 3.83: 16143 3.83 - 4.36: 20846 4.36 - 4.90: 34252 Nonbonded interactions: 81743 Sorted by model distance: nonbonded pdb=" OE1 GLN B 85 " pdb="NA NA B 803 " model vdw 2.218 2.470 nonbonded pdb=" OE1 GLN A 85 " pdb="NA NA A 803 " model vdw 2.218 2.470 nonbonded pdb=" O HOH B 933 " pdb=" O HOH B 934 " model vdw 2.246 2.440 nonbonded pdb=" O HOH A 933 " pdb=" O HOH A 934 " model vdw 2.246 2.440 nonbonded pdb=" O HOH B 921 " pdb=" O HOH B 938 " model vdw 2.250 2.440 ... (remaining 81738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.830 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: 7.450 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 29.570 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 52.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.007 0.066 10096 Z= 0.456 Angle : 0.868 13.642 13694 Z= 0.495 Chirality : 0.056 0.363 1612 Planarity : 0.007 0.067 1688 Dihedral : 15.519 89.256 3580 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.29 % Favored : 95.56 % Rotamer: Outliers : 6.10 % Allowed : 3.88 % Favored : 90.02 % 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: -5.35 (0.16), residues: 1260 helix: -4.18 (0.07), residues: 774 sheet: 0.66 (0.67), residues: 56 loop : -2.42 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 61 HIS 0.004 0.001 HIS A 385 PHE 0.018 0.002 PHE B 499 TYR 0.014 0.002 TYR B 539 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 156 time to evaluate : 1.137 Fit side-chains REVERT: A 317 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8060 (mtp85) REVERT: A 333 MET cc_start: 0.8621 (mtt) cc_final: 0.8107 (mtt) REVERT: A 527 GLN cc_start: 0.8262 (tp-100) cc_final: 0.8038 (tp40) REVERT: A 669 MET cc_start: 0.8581 (mtp) cc_final: 0.8246 (mtp) REVERT: B 317 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8059 (mtp85) REVERT: B 333 MET cc_start: 0.8623 (mtt) cc_final: 0.8108 (mtt) REVERT: B 527 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8036 (tp40) REVERT: B 669 MET cc_start: 0.8586 (mtp) cc_final: 0.8250 (mtp) outliers start: 66 outliers final: 6 residues processed: 194 average time/residue: 1.0536 time to fit residues: 221.7999 Evaluate side-chains 98 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 720 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 191 GLN A 366 ASN A 376 ASN A 385 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 559 GLN B 102 ASN B 191 GLN B 366 ASN B 376 ASN B 385 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 559 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10096 Z= 0.173 Angle : 0.561 6.192 13694 Z= 0.304 Chirality : 0.042 0.127 1612 Planarity : 0.006 0.047 1688 Dihedral : 5.817 51.273 1356 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.48 % Allowed : 9.06 % Favored : 89.46 % 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: -1.85 (0.21), residues: 1260 helix: -1.01 (0.16), residues: 776 sheet: 1.34 (0.66), residues: 54 loop : -1.74 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS B 385 PHE 0.016 0.001 PHE B 24 TYR 0.011 0.001 TYR A 159 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.203 Fit side-chains REVERT: A 190 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7939 (tmm) REVERT: A 287 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: A 527 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8096 (tp40) REVERT: B 190 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7940 (tmm) REVERT: B 287 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: B 527 GLN cc_start: 0.8351 (tp-100) cc_final: 0.8093 (tp40) outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 1.3188 time to fit residues: 160.0226 Evaluate side-chains 96 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 720 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.0060 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 663 HIS B 501 ASN B 663 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10096 Z= 0.330 Angle : 0.606 6.123 13694 Z= 0.327 Chirality : 0.046 0.158 1612 Planarity : 0.005 0.055 1688 Dihedral : 5.340 27.062 1350 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.22 % Allowed : 9.24 % Favored : 88.54 % 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: -0.31 (0.23), residues: 1260 helix: 0.43 (0.18), residues: 794 sheet: 1.28 (0.67), residues: 56 loop : -1.60 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 61 HIS 0.006 0.001 HIS A 385 PHE 0.018 0.002 PHE B 499 TYR 0.012 0.002 TYR B 514 ARG 0.005 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.120 Fit side-chains REVERT: A 168 GLU cc_start: 0.7825 (tp30) cc_final: 0.7494 (tp30) REVERT: A 190 MET cc_start: 0.8340 (ttp) cc_final: 0.7968 (tmm) REVERT: A 527 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8157 (tp40) REVERT: B 168 GLU cc_start: 0.7825 (tp30) cc_final: 0.7494 (tp30) REVERT: B 190 MET cc_start: 0.8342 (ttp) cc_final: 0.7966 (tmm) REVERT: B 527 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8155 (tp40) outliers start: 24 outliers final: 16 residues processed: 114 average time/residue: 1.1343 time to fit residues: 140.1989 Evaluate side-chains 104 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 720 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8363 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10096 Z= 0.191 Angle : 0.524 5.985 13694 Z= 0.281 Chirality : 0.042 0.147 1612 Planarity : 0.004 0.048 1688 Dihedral : 4.845 22.310 1350 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.85 % Allowed : 9.61 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1260 helix: 1.30 (0.19), residues: 782 sheet: 1.80 (0.67), residues: 54 loop : -1.36 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.005 0.001 HIS B 385 PHE 0.014 0.001 PHE A 24 TYR 0.012 0.001 TYR B 159 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.133 Fit side-chains REVERT: A 48 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8612 (mm) REVERT: A 168 GLU cc_start: 0.7824 (tp30) cc_final: 0.7530 (tp30) REVERT: A 527 GLN cc_start: 0.8362 (tp-100) cc_final: 0.8057 (tp40) REVERT: B 48 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8611 (mm) REVERT: B 168 GLU cc_start: 0.7824 (tp30) cc_final: 0.7530 (tp30) REVERT: B 527 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8054 (tp40) outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 1.1118 time to fit residues: 135.0401 Evaluate side-chains 102 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10096 Z= 0.189 Angle : 0.516 6.094 13694 Z= 0.276 Chirality : 0.042 0.141 1612 Planarity : 0.004 0.047 1688 Dihedral : 4.712 21.557 1348 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.66 % Allowed : 10.72 % Favored : 87.62 % 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: 1.17 (0.24), residues: 1260 helix: 1.74 (0.19), residues: 772 sheet: 1.63 (0.70), residues: 56 loop : -1.14 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.005 0.001 HIS A 385 PHE 0.013 0.001 PHE B 24 TYR 0.012 0.001 TYR B 159 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.153 Fit side-chains REVERT: A 147 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8111 (mtpp) REVERT: A 168 GLU cc_start: 0.7805 (tp30) cc_final: 0.7494 (tp30) REVERT: A 527 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8004 (tp40) REVERT: B 147 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8117 (mtpp) REVERT: B 168 GLU cc_start: 0.7804 (tp30) cc_final: 0.7496 (tp30) REVERT: B 527 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8003 (tp40) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 1.1894 time to fit residues: 141.2528 Evaluate side-chains 106 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS B 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10096 Z= 0.164 Angle : 0.498 6.050 13694 Z= 0.265 Chirality : 0.042 0.143 1612 Planarity : 0.004 0.044 1688 Dihedral : 4.559 20.408 1348 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.03 % Allowed : 10.91 % Favored : 87.06 % 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: 1.50 (0.24), residues: 1260 helix: 2.06 (0.19), residues: 768 sheet: 1.63 (0.70), residues: 56 loop : -1.09 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 61 HIS 0.004 0.001 HIS A 385 PHE 0.012 0.001 PHE B 24 TYR 0.010 0.001 TYR A 454 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.109 Fit side-chains REVERT: A 48 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 168 GLU cc_start: 0.7794 (tp30) cc_final: 0.7473 (tp30) REVERT: A 280 ILE cc_start: 0.4788 (OUTLIER) cc_final: 0.4500 (pt) REVERT: A 527 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7940 (tp40) REVERT: B 48 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8616 (mm) REVERT: B 168 GLU cc_start: 0.7793 (tp30) cc_final: 0.7477 (tp30) REVERT: B 280 ILE cc_start: 0.4781 (OUTLIER) cc_final: 0.4495 (pt) REVERT: B 527 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7939 (tp40) outliers start: 22 outliers final: 12 residues processed: 114 average time/residue: 1.1063 time to fit residues: 136.9453 Evaluate side-chains 108 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10096 Z= 0.196 Angle : 0.516 6.131 13694 Z= 0.274 Chirality : 0.042 0.137 1612 Planarity : 0.004 0.044 1688 Dihedral : 4.609 20.031 1348 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 11.28 % Favored : 86.88 % 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: 1.60 (0.24), residues: 1260 helix: 2.14 (0.19), residues: 770 sheet: 1.60 (0.70), residues: 56 loop : -1.05 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.004 0.001 HIS B 385 PHE 0.013 0.001 PHE B 499 TYR 0.009 0.001 TYR A 454 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.134 Fit side-chains REVERT: A 147 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8123 (mtpp) REVERT: A 168 GLU cc_start: 0.7817 (tp30) cc_final: 0.7492 (tp30) REVERT: A 527 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7921 (tp40) REVERT: B 147 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8128 (mtpp) REVERT: B 168 GLU cc_start: 0.7816 (tp30) cc_final: 0.7492 (tp30) REVERT: B 527 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7934 (tp40) outliers start: 20 outliers final: 14 residues processed: 108 average time/residue: 1.1519 time to fit residues: 134.9342 Evaluate side-chains 106 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8375 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10096 Z= 0.239 Angle : 0.540 6.354 13694 Z= 0.288 Chirality : 0.044 0.141 1612 Planarity : 0.004 0.043 1688 Dihedral : 4.754 19.793 1348 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.48 % Allowed : 12.20 % Favored : 86.32 % 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: 1.59 (0.24), residues: 1260 helix: 2.11 (0.19), residues: 770 sheet: 1.60 (0.70), residues: 56 loop : -1.02 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 61 HIS 0.005 0.001 HIS B 385 PHE 0.015 0.001 PHE B 499 TYR 0.013 0.001 TYR B 159 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.055 Fit side-chains REVERT: A 168 GLU cc_start: 0.7831 (tp30) cc_final: 0.7509 (tp30) REVERT: A 287 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: A 527 GLN cc_start: 0.8269 (tp-100) cc_final: 0.8030 (tm-30) REVERT: B 168 GLU cc_start: 0.7831 (tp30) cc_final: 0.7512 (tp30) REVERT: B 287 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: B 527 GLN cc_start: 0.8269 (tp-100) cc_final: 0.8029 (tm-30) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 1.2042 time to fit residues: 133.0577 Evaluate side-chains 102 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10096 Z= 0.148 Angle : 0.492 7.897 13694 Z= 0.259 Chirality : 0.041 0.135 1612 Planarity : 0.004 0.039 1688 Dihedral : 4.441 20.136 1348 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.29 % Allowed : 12.38 % Favored : 86.32 % 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: 1.91 (0.25), residues: 1260 helix: 2.44 (0.19), residues: 762 sheet: 1.59 (0.70), residues: 56 loop : -0.97 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.004 0.001 HIS A 385 PHE 0.012 0.001 PHE B 24 TYR 0.010 0.001 TYR B 454 ARG 0.001 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.035 Fit side-chains REVERT: A 168 GLU cc_start: 0.7790 (tp30) cc_final: 0.7464 (tp30) REVERT: A 527 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7960 (tm-30) REVERT: B 168 GLU cc_start: 0.7788 (tp30) cc_final: 0.7461 (tp30) REVERT: B 527 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7959 (tm-30) outliers start: 14 outliers final: 7 residues processed: 107 average time/residue: 1.1758 time to fit residues: 136.0889 Evaluate side-chains 99 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10096 Z= 0.272 Angle : 0.560 8.295 13694 Z= 0.296 Chirality : 0.045 0.137 1612 Planarity : 0.004 0.042 1688 Dihedral : 4.728 20.006 1348 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.83 % Allowed : 12.94 % Favored : 86.23 % 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: 1.70 (0.24), residues: 1260 helix: 2.19 (0.19), residues: 770 sheet: 1.54 (0.71), residues: 56 loop : -0.94 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 61 HIS 0.005 0.001 HIS A 385 PHE 0.016 0.001 PHE A 499 TYR 0.011 0.001 TYR A 514 ARG 0.004 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.160 Fit side-chains REVERT: A 168 GLU cc_start: 0.7841 (tp30) cc_final: 0.7521 (tp30) REVERT: A 287 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: A 527 GLN cc_start: 0.8243 (tp-100) cc_final: 0.8003 (tm-30) REVERT: B 168 GLU cc_start: 0.7840 (tp30) cc_final: 0.7521 (tp30) REVERT: B 287 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: B 527 GLN cc_start: 0.8242 (tp-100) cc_final: 0.8001 (tm-30) outliers start: 9 outliers final: 6 residues processed: 98 average time/residue: 1.2535 time to fit residues: 132.5304 Evaluate side-chains 99 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.0040 chunk 104 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.079271 restraints weight = 13478.959| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.83 r_work: 0.2762 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10096 Z= 0.166 Angle : 0.510 8.557 13694 Z= 0.269 Chirality : 0.042 0.135 1612 Planarity : 0.004 0.038 1688 Dihedral : 4.497 20.437 1348 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.55 % Allowed : 13.03 % Favored : 86.41 % 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: 1.91 (0.25), residues: 1260 helix: 2.39 (0.19), residues: 768 sheet: 1.54 (0.71), residues: 56 loop : -0.89 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS A 385 PHE 0.012 0.001 PHE B 24 TYR 0.010 0.001 TYR B 454 ARG 0.001 0.000 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.51 seconds wall clock time: 58 minutes 43.88 seconds (3523.88 seconds total)