Starting phenix.real_space_refine on Thu Mar 14 16:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/03_2024/6qvb_4646.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/03_2024/6qvb_4646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/03_2024/6qvb_4646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/03_2024/6qvb_4646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/03_2024/6qvb_4646.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/03_2024/6qvb_4646.pdb" } resolution = 4.34 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6109 2.51 5 N 1482 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 199": "NH1" <-> "NH2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 670": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9237 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4617 Classifications: {'peptide': 596} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 566} Chain breaks: 3 Chain: "A" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4620 Classifications: {'peptide': 597} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 567} Chain breaks: 3 Time building chain proxies: 5.00, per 1000 atoms: 0.54 Number of scatterers: 9237 At special positions: 0 Unit cell: (110.21, 118.77, 108.07, 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 70 16.00 O 1576 8.00 N 1482 7.00 C 6109 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 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 66.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'B' and resid 115 through 153 Processing helix chain 'B' and resid 158 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.499A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.283A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 323 removed outlier: 3.778A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 375 removed outlier: 3.717A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.546A pdb=" N LEU B 392 " --> pdb=" O HIS B 389 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 389 through 393' Processing helix chain 'B' and resid 394 through 404 removed outlier: 3.520A pdb=" N THR B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 455 through 477 removed outlier: 4.867A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.613A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.881A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 585 removed outlier: 3.723A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 632 removed outlier: 4.074A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 863 through 872 removed outlier: 3.947A pdb=" N GLY B 872 " --> pdb=" O LYS B 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 153 Processing helix chain 'A' and resid 158 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.492A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 209 through 224 removed outlier: 4.269A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 323 removed outlier: 3.872A pdb=" N TYR A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 375 removed outlier: 3.692A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.549A pdb=" N LEU A 392 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 393 " --> pdb=" O ARG A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 393' Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.670A pdb=" N THR A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 455 through 477 removed outlier: 4.763A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 4.738A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 4.060A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.696A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 632 removed outlier: 4.082A pdb=" N THR A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 872 removed outlier: 3.830A pdb=" N LEU A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640 removed outlier: 6.078A pdb=" N LEU B 637 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 651 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 639 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 5.978A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640 removed outlier: 6.020A pdb=" N LEU A 637 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 651 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 639 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 5.979A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1629 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: 2.52 Time building geometry restraints manager: 4.03 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: 2735 1.34 - 1.46: 2230 1.46 - 1.58: 4384 1.58 - 1.70: 2 1.70 - 1.82: 116 Bond restraints: 9467 Sorted by residual: bond pdb=" CB MET B 414 " pdb=" CG MET B 414 " ideal model delta sigma weight residual 1.520 1.389 0.131 3.00e-02 1.11e+03 1.91e+01 bond pdb=" CB TYR A 302 " pdb=" CG TYR A 302 " ideal model delta sigma weight residual 1.512 1.429 0.083 2.20e-02 2.07e+03 1.42e+01 bond pdb=" CG TYR A 302 " pdb=" CD1 TYR A 302 " ideal model delta sigma weight residual 1.389 1.320 0.069 2.10e-02 2.27e+03 1.07e+01 bond pdb=" CE1 TYR A 302 " pdb=" CZ TYR A 302 " ideal model delta sigma weight residual 1.378 1.304 0.074 2.40e-02 1.74e+03 9.49e+00 bond pdb=" CD1 TYR A 302 " pdb=" CE1 TYR A 302 " ideal model delta sigma weight residual 1.382 1.291 0.091 3.00e-02 1.11e+03 9.26e+00 ... (remaining 9462 not shown) Histogram of bond angle deviations from ideal: 91.50 - 100.73: 33 100.73 - 109.95: 1925 109.95 - 119.17: 6055 119.17 - 128.39: 4729 128.39 - 137.61: 119 Bond angle restraints: 12861 Sorted by residual: angle pdb=" C TYR B 589 " pdb=" N LEU B 593 " pdb=" CA LEU B 593 " ideal model delta sigma weight residual 121.70 135.34 -13.64 1.80e+00 3.09e-01 5.74e+01 angle pdb=" C TYR A 589 " pdb=" N LEU A 593 " pdb=" CA LEU A 593 " ideal model delta sigma weight residual 121.70 135.33 -13.63 1.80e+00 3.09e-01 5.73e+01 angle pdb=" CA TRP A 469 " pdb=" CB TRP A 469 " pdb=" CG TRP A 469 " ideal model delta sigma weight residual 113.60 127.33 -13.73 1.90e+00 2.77e-01 5.22e+01 angle pdb=" CA TYR B 589 " pdb=" C TYR B 589 " pdb=" N LEU B 593 " ideal model delta sigma weight residual 116.84 128.50 -11.66 1.71e+00 3.42e-01 4.65e+01 angle pdb=" CA TYR A 589 " pdb=" C TYR A 589 " pdb=" N LEU A 593 " ideal model delta sigma weight residual 116.84 128.38 -11.54 1.71e+00 3.42e-01 4.55e+01 ... (remaining 12856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 4914 14.51 - 29.02: 466 29.02 - 43.53: 120 43.53 - 58.04: 23 58.04 - 72.55: 4 Dihedral angle restraints: 5527 sinusoidal: 2104 harmonic: 3423 Sorted by residual: dihedral pdb=" CA LYS A 324 " pdb=" C LYS A 324 " pdb=" N ASP A 325 " pdb=" CA ASP A 325 " ideal model delta harmonic sigma weight residual 180.00 -137.16 -42.84 0 5.00e+00 4.00e-02 7.34e+01 dihedral pdb=" CA LYS B 324 " pdb=" C LYS B 324 " pdb=" N ASP B 325 " pdb=" CA ASP B 325 " ideal model delta harmonic sigma weight residual -180.00 -137.26 -42.74 0 5.00e+00 4.00e-02 7.31e+01 dihedral pdb=" CA ARG B 670 " pdb=" C ARG B 670 " pdb=" N LEU B 671 " pdb=" CA LEU B 671 " ideal model delta harmonic sigma weight residual 180.00 -137.73 -42.27 0 5.00e+00 4.00e-02 7.15e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1183 0.094 - 0.188: 270 0.188 - 0.282: 47 0.282 - 0.377: 9 0.377 - 0.471: 10 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CG LEU B 671 " pdb=" CB LEU B 671 " pdb=" CD1 LEU B 671 " pdb=" CD2 LEU B 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA PHE B 488 " pdb=" N PHE B 488 " pdb=" C PHE B 488 " pdb=" CB PHE B 488 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 1516 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 517 " 0.068 2.00e-02 2.50e+03 5.24e-02 5.49e+01 pdb=" CG TYR B 517 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 TYR B 517 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 517 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 517 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 517 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 517 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR B 517 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " 0.068 2.00e-02 2.50e+03 5.22e-02 5.46e+01 pdb=" CG TYR A 517 " -0.126 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 469 " -0.056 2.00e-02 2.50e+03 4.11e-02 4.22e+01 pdb=" CG TRP A 469 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 TRP A 469 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 469 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 469 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 469 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 469 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 469 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 469 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 469 " -0.004 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 535 2.70 - 3.25: 9654 3.25 - 3.80: 15800 3.80 - 4.35: 18494 4.35 - 4.90: 29057 Nonbonded interactions: 73540 Sorted by model distance: nonbonded pdb=" OH TYR B 302 " pdb=" O GLU A 291 " model vdw 2.153 2.440 nonbonded pdb=" O ILE B 401 " pdb=" OG1 THR B 405 " model vdw 2.156 2.440 nonbonded pdb=" O CYS A 179 " pdb=" OG SER A 183 " model vdw 2.194 2.440 nonbonded pdb=" O CYS B 179 " pdb=" OG SER B 183 " model vdw 2.194 2.440 nonbonded pdb=" O CYS A 546 " pdb=" OG1 THR A 550 " model vdw 2.227 2.440 ... (remaining 73535 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' and (resid 115 through 671 or resid 819 through 872)) selection = (chain 'B' and (resid 115 through 671 or resid 819 through 872)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 5.470 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.160 Find NCS groups from input model: 0.590 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.010 0.131 9467 Z= 0.621 Angle : 1.720 21.313 12861 Z= 0.891 Chirality : 0.090 0.471 1519 Planarity : 0.012 0.073 1573 Dihedral : 12.748 72.553 3325 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.28 % Favored : 89.55 % Rotamer: Outliers : 3.10 % Allowed : 8.91 % Favored : 87.99 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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: -4.45 (0.19), residues: 1177 helix: -2.20 (0.15), residues: 740 sheet: -3.20 (0.60), residues: 44 loop : -4.22 (0.23), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.008 TRP A 469 HIS 0.017 0.003 HIS A 555 PHE 0.073 0.006 PHE B 341 TYR 0.127 0.007 TYR B 517 ARG 0.017 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 LEU cc_start: 0.9691 (mt) cc_final: 0.9371 (mt) REVERT: B 267 LEU cc_start: 0.9701 (mp) cc_final: 0.9500 (tt) REVERT: B 307 PHE cc_start: 0.9541 (t80) cc_final: 0.9098 (t80) REVERT: B 417 GLU cc_start: 0.9011 (tt0) cc_final: 0.8712 (tm-30) REVERT: B 464 PHE cc_start: 0.9589 (t80) cc_final: 0.9352 (t80) REVERT: B 559 MET cc_start: 0.9560 (ptp) cc_final: 0.9270 (ptm) REVERT: B 565 LEU cc_start: 0.9672 (mt) cc_final: 0.9365 (tt) REVERT: B 660 LEU cc_start: 0.9761 (tt) cc_final: 0.9554 (mt) REVERT: B 854 MET cc_start: 0.8638 (tmm) cc_final: 0.8354 (tmm) REVERT: A 128 MET cc_start: 0.9708 (tpp) cc_final: 0.9052 (tpp) REVERT: A 143 LEU cc_start: 0.9459 (tp) cc_final: 0.9067 (tp) REVERT: A 399 PHE cc_start: 0.8710 (m-80) cc_final: 0.8463 (m-80) REVERT: A 417 GLU cc_start: 0.9197 (tt0) cc_final: 0.8670 (tm-30) REVERT: A 419 MET cc_start: 0.9507 (mmp) cc_final: 0.9178 (mmt) REVERT: A 466 MET cc_start: 0.9174 (tpt) cc_final: 0.8961 (tpt) REVERT: A 473 VAL cc_start: 0.9609 (p) cc_final: 0.9392 (m) REVERT: A 488 PHE cc_start: 0.9396 (m-10) cc_final: 0.9189 (m-10) REVERT: A 559 MET cc_start: 0.9558 (ptp) cc_final: 0.9253 (ptm) REVERT: A 564 ILE cc_start: 0.9757 (mm) cc_final: 0.9505 (mm) REVERT: A 565 LEU cc_start: 0.9633 (mt) cc_final: 0.9215 (tt) REVERT: A 854 MET cc_start: 0.8894 (tmm) cc_final: 0.8600 (tmm) outliers start: 31 outliers final: 9 residues processed: 265 average time/residue: 0.1947 time to fit residues: 72.6676 Evaluate side-chains 165 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS B 379 HIS B 823 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS A 379 HIS A 823 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9467 Z= 0.257 Angle : 0.916 10.918 12861 Z= 0.479 Chirality : 0.050 0.315 1519 Planarity : 0.006 0.049 1573 Dihedral : 8.181 56.504 1260 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.40 % Allowed : 5.91 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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 (0.22), residues: 1177 helix: -0.57 (0.17), residues: 746 sheet: -2.58 (0.67), residues: 44 loop : -3.84 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 469 HIS 0.006 0.001 HIS B 369 PHE 0.060 0.003 PHE B 488 TYR 0.022 0.002 TYR A 517 ARG 0.008 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 246 LEU cc_start: 0.9504 (tp) cc_final: 0.9146 (mt) REVERT: B 250 MET cc_start: 0.9226 (tmm) cc_final: 0.8933 (tmm) REVERT: B 267 LEU cc_start: 0.9739 (mp) cc_final: 0.9493 (tp) REVERT: B 307 PHE cc_start: 0.9467 (t80) cc_final: 0.9210 (t80) REVERT: B 410 MET cc_start: 0.9686 (tpt) cc_final: 0.9323 (tpp) REVERT: B 414 MET cc_start: 0.9388 (tmm) cc_final: 0.8900 (tmm) REVERT: B 417 GLU cc_start: 0.9018 (tt0) cc_final: 0.8543 (tm-30) REVERT: B 548 GLU cc_start: 0.8618 (pp20) cc_final: 0.8238 (pp20) REVERT: B 559 MET cc_start: 0.9415 (ptp) cc_final: 0.9169 (ptm) REVERT: B 560 MET cc_start: 0.9334 (mpp) cc_final: 0.9120 (mpp) REVERT: B 565 LEU cc_start: 0.9604 (mt) cc_final: 0.9225 (tt) REVERT: B 609 MET cc_start: 0.8632 (mmp) cc_final: 0.8214 (mmp) REVERT: B 646 MET cc_start: 0.9671 (mmp) cc_final: 0.9442 (mmm) REVERT: A 235 PHE cc_start: 0.8719 (t80) cc_final: 0.7937 (t80) REVERT: A 250 MET cc_start: 0.9178 (tmm) cc_final: 0.8881 (tmm) REVERT: A 399 PHE cc_start: 0.8746 (m-80) cc_final: 0.8255 (m-80) REVERT: A 410 MET cc_start: 0.9696 (tpt) cc_final: 0.9307 (tpp) REVERT: A 488 PHE cc_start: 0.9256 (m-10) cc_final: 0.8598 (m-10) REVERT: A 548 GLU cc_start: 0.8592 (pp20) cc_final: 0.8266 (pp20) REVERT: A 559 MET cc_start: 0.9502 (ptp) cc_final: 0.9300 (ptm) REVERT: A 564 ILE cc_start: 0.9683 (mm) cc_final: 0.9480 (mm) REVERT: A 565 LEU cc_start: 0.9561 (mt) cc_final: 0.9180 (tt) REVERT: A 609 MET cc_start: 0.8859 (mmp) cc_final: 0.8427 (mmp) REVERT: A 646 MET cc_start: 0.9619 (mmp) cc_final: 0.9320 (mtm) REVERT: A 854 MET cc_start: 0.8705 (tmm) cc_final: 0.8438 (tmm) outliers start: 4 outliers final: 2 residues processed: 209 average time/residue: 0.1740 time to fit residues: 53.1227 Evaluate side-chains 158 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9467 Z= 0.243 Angle : 0.865 10.038 12861 Z= 0.446 Chirality : 0.048 0.235 1519 Planarity : 0.005 0.041 1573 Dihedral : 7.635 57.009 1260 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.84 (0.23), residues: 1177 helix: 0.05 (0.18), residues: 763 sheet: -2.32 (0.73), residues: 44 loop : -3.85 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 469 HIS 0.006 0.001 HIS B 379 PHE 0.048 0.003 PHE B 488 TYR 0.017 0.002 TYR B 622 ARG 0.002 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.116 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: B 143 LEU cc_start: 0.9321 (tp) cc_final: 0.9061 (pp) REVERT: B 235 PHE cc_start: 0.8915 (t80) cc_final: 0.8102 (t80) REVERT: B 250 MET cc_start: 0.9254 (tmm) cc_final: 0.8953 (tmm) REVERT: B 267 LEU cc_start: 0.9729 (mp) cc_final: 0.9475 (tt) REVERT: B 307 PHE cc_start: 0.9474 (t80) cc_final: 0.9216 (t80) REVERT: B 373 MET cc_start: 0.9233 (mmp) cc_final: 0.8767 (mtp) REVERT: B 410 MET cc_start: 0.9656 (tpt) cc_final: 0.9322 (tpp) REVERT: B 414 MET cc_start: 0.9273 (tmm) cc_final: 0.8810 (tmm) REVERT: B 565 LEU cc_start: 0.9539 (mt) cc_final: 0.9136 (tt) REVERT: B 609 MET cc_start: 0.8861 (mmp) cc_final: 0.8439 (mmp) REVERT: B 646 MET cc_start: 0.9692 (mmp) cc_final: 0.9475 (mmm) REVERT: A 128 MET cc_start: 0.9418 (mtm) cc_final: 0.9061 (mtp) REVERT: A 143 LEU cc_start: 0.9376 (tp) cc_final: 0.8995 (pp) REVERT: A 235 PHE cc_start: 0.8833 (t80) cc_final: 0.7930 (t80) REVERT: A 339 MET cc_start: 0.8873 (pmm) cc_final: 0.8530 (pmm) REVERT: A 399 PHE cc_start: 0.8853 (m-80) cc_final: 0.8269 (m-80) REVERT: A 410 MET cc_start: 0.9658 (tpt) cc_final: 0.9323 (tpp) REVERT: A 414 MET cc_start: 0.9132 (tmm) cc_final: 0.8833 (tmm) REVERT: A 466 MET cc_start: 0.9357 (tpt) cc_final: 0.9024 (tpt) REVERT: A 485 MET cc_start: 0.9527 (mmp) cc_final: 0.9130 (mmm) REVERT: A 488 PHE cc_start: 0.9261 (m-10) cc_final: 0.8951 (m-10) REVERT: A 548 GLU cc_start: 0.8550 (pp20) cc_final: 0.8230 (pp20) REVERT: A 564 ILE cc_start: 0.9667 (mm) cc_final: 0.9459 (mm) REVERT: A 565 LEU cc_start: 0.9544 (mt) cc_final: 0.9166 (tt) REVERT: A 609 MET cc_start: 0.8897 (mmp) cc_final: 0.8497 (mmp) REVERT: A 646 MET cc_start: 0.9636 (mmp) cc_final: 0.9323 (mtp) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1722 time to fit residues: 50.4660 Evaluate side-chains 156 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 0.0000 chunk 55 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9467 Z= 0.251 Angle : 0.862 11.271 12861 Z= 0.444 Chirality : 0.047 0.193 1519 Planarity : 0.004 0.038 1573 Dihedral : 7.318 53.658 1260 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.30 % Allowed : 6.01 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.33 (0.24), residues: 1177 helix: 0.48 (0.18), residues: 761 sheet: -2.10 (0.80), residues: 44 loop : -3.71 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 469 HIS 0.004 0.001 HIS B 451 PHE 0.045 0.002 PHE B 488 TYR 0.049 0.003 TYR A 589 ARG 0.002 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 0.835 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: B 127 LEU cc_start: 0.9703 (pp) cc_final: 0.9273 (pp) REVERT: B 128 MET cc_start: 0.9634 (mmp) cc_final: 0.9401 (mmm) REVERT: B 143 LEU cc_start: 0.9373 (tp) cc_final: 0.9078 (pp) REVERT: B 174 PHE cc_start: 0.9603 (m-10) cc_final: 0.9354 (m-80) REVERT: B 235 PHE cc_start: 0.8590 (t80) cc_final: 0.8097 (t80) REVERT: B 250 MET cc_start: 0.9232 (tmm) cc_final: 0.9016 (tmm) REVERT: B 267 LEU cc_start: 0.9758 (mp) cc_final: 0.9500 (tp) REVERT: B 307 PHE cc_start: 0.9489 (t80) cc_final: 0.9268 (t80) REVERT: B 339 MET cc_start: 0.8864 (ptp) cc_final: 0.8617 (ptt) REVERT: B 374 LEU cc_start: 0.9213 (tp) cc_final: 0.9007 (mt) REVERT: B 410 MET cc_start: 0.9631 (tpt) cc_final: 0.9310 (tpp) REVERT: B 414 MET cc_start: 0.9238 (tmm) cc_final: 0.8807 (tmm) REVERT: B 470 MET cc_start: 0.8781 (ppp) cc_final: 0.8521 (ppp) REVERT: B 609 MET cc_start: 0.8825 (mmp) cc_final: 0.8526 (mmp) REVERT: B 646 MET cc_start: 0.9691 (mmp) cc_final: 0.9473 (mmm) REVERT: A 128 MET cc_start: 0.9409 (mtm) cc_final: 0.9043 (mtp) REVERT: A 178 PHE cc_start: 0.9396 (m-10) cc_final: 0.9036 (m-80) REVERT: A 235 PHE cc_start: 0.8764 (t80) cc_final: 0.7941 (t80) REVERT: A 339 MET cc_start: 0.8894 (pmm) cc_final: 0.8642 (pmm) REVERT: A 399 PHE cc_start: 0.8858 (m-80) cc_final: 0.8296 (m-80) REVERT: A 410 MET cc_start: 0.9646 (tpt) cc_final: 0.9328 (tpp) REVERT: A 466 MET cc_start: 0.9367 (tpt) cc_final: 0.8896 (tpt) REVERT: A 485 MET cc_start: 0.9569 (mmp) cc_final: 0.9242 (mmm) REVERT: A 488 PHE cc_start: 0.9237 (m-10) cc_final: 0.8987 (m-10) REVERT: A 559 MET cc_start: 0.9656 (ptm) cc_final: 0.8991 (ppp) REVERT: A 560 MET cc_start: 0.9637 (mtm) cc_final: 0.9026 (mtm) REVERT: A 609 MET cc_start: 0.8825 (mmp) cc_final: 0.8452 (mmp) REVERT: A 646 MET cc_start: 0.9640 (mmp) cc_final: 0.9338 (mtp) outliers start: 3 outliers final: 0 residues processed: 194 average time/residue: 0.1697 time to fit residues: 48.2046 Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 97 optimal weight: 0.0770 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9467 Z= 0.204 Angle : 0.845 10.204 12861 Z= 0.423 Chirality : 0.047 0.181 1519 Planarity : 0.004 0.041 1573 Dihedral : 6.886 45.305 1260 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -0.98 (0.24), residues: 1177 helix: 0.79 (0.18), residues: 759 sheet: -2.11 (0.90), residues: 34 loop : -3.62 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 469 HIS 0.003 0.001 HIS B 664 PHE 0.043 0.002 PHE B 488 TYR 0.028 0.002 TYR A 589 ARG 0.003 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 LEU cc_start: 0.9342 (tp) cc_final: 0.9040 (pp) REVERT: B 174 PHE cc_start: 0.9603 (m-10) cc_final: 0.9368 (m-80) REVERT: B 235 PHE cc_start: 0.8554 (t80) cc_final: 0.8017 (t80) REVERT: B 267 LEU cc_start: 0.9776 (mp) cc_final: 0.9522 (tp) REVERT: B 307 PHE cc_start: 0.9469 (t80) cc_final: 0.8717 (t80) REVERT: B 339 MET cc_start: 0.8724 (ptp) cc_final: 0.8409 (ptp) REVERT: B 374 LEU cc_start: 0.9070 (tp) cc_final: 0.8830 (mt) REVERT: B 399 PHE cc_start: 0.9002 (m-80) cc_final: 0.8466 (m-80) REVERT: B 410 MET cc_start: 0.9595 (tpt) cc_final: 0.9262 (tpp) REVERT: B 414 MET cc_start: 0.9247 (tmm) cc_final: 0.8930 (tmm) REVERT: B 470 MET cc_start: 0.8756 (ppp) cc_final: 0.8447 (ppp) REVERT: B 560 MET cc_start: 0.9311 (mpp) cc_final: 0.9072 (mpp) REVERT: B 609 MET cc_start: 0.8905 (mmp) cc_final: 0.8549 (mmp) REVERT: B 646 MET cc_start: 0.9697 (mmp) cc_final: 0.9466 (mmm) REVERT: A 128 MET cc_start: 0.9384 (mtm) cc_final: 0.9016 (mtp) REVERT: A 178 PHE cc_start: 0.9373 (m-10) cc_final: 0.9041 (m-80) REVERT: A 235 PHE cc_start: 0.8672 (t80) cc_final: 0.7751 (t80) REVERT: A 339 MET cc_start: 0.8960 (pmm) cc_final: 0.8632 (pmm) REVERT: A 399 PHE cc_start: 0.8851 (m-80) cc_final: 0.8325 (m-80) REVERT: A 404 PHE cc_start: 0.8900 (p90) cc_final: 0.8529 (p90) REVERT: A 410 MET cc_start: 0.9594 (tpt) cc_final: 0.9241 (tpp) REVERT: A 414 MET cc_start: 0.9094 (tmm) cc_final: 0.8890 (tmm) REVERT: A 466 MET cc_start: 0.9283 (tpt) cc_final: 0.8856 (tpt) REVERT: A 485 MET cc_start: 0.9562 (mmp) cc_final: 0.9276 (mmm) REVERT: A 488 PHE cc_start: 0.9274 (m-10) cc_final: 0.8974 (m-10) REVERT: A 560 MET cc_start: 0.9653 (mtm) cc_final: 0.9438 (mtp) REVERT: A 609 MET cc_start: 0.8905 (mmp) cc_final: 0.8481 (mmp) REVERT: A 646 MET cc_start: 0.9638 (mmp) cc_final: 0.9343 (mtp) outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.1679 time to fit residues: 49.4296 Evaluate side-chains 150 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9467 Z= 0.207 Angle : 0.827 9.514 12861 Z= 0.414 Chirality : 0.046 0.183 1519 Planarity : 0.004 0.069 1573 Dihedral : 6.587 40.370 1260 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.69 (0.25), residues: 1177 helix: 0.97 (0.19), residues: 763 sheet: -2.35 (1.03), residues: 24 loop : -3.38 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 469 HIS 0.004 0.001 HIS B 451 PHE 0.025 0.002 PHE B 120 TYR 0.018 0.002 TYR A 589 ARG 0.002 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9397 (mtm) cc_final: 0.9141 (mpp) REVERT: B 174 PHE cc_start: 0.9631 (m-10) cc_final: 0.9426 (m-80) REVERT: B 235 PHE cc_start: 0.8747 (t80) cc_final: 0.8071 (t80) REVERT: B 246 LEU cc_start: 0.9292 (tp) cc_final: 0.9083 (tp) REVERT: B 250 MET cc_start: 0.8717 (mmp) cc_final: 0.8445 (mmm) REVERT: B 267 LEU cc_start: 0.9722 (mp) cc_final: 0.9475 (tt) REVERT: B 374 LEU cc_start: 0.9179 (tp) cc_final: 0.8939 (mt) REVERT: B 399 PHE cc_start: 0.9004 (m-80) cc_final: 0.8524 (m-80) REVERT: B 410 MET cc_start: 0.9579 (tpt) cc_final: 0.9242 (tpp) REVERT: B 414 MET cc_start: 0.9222 (tmm) cc_final: 0.8862 (tmm) REVERT: B 470 MET cc_start: 0.8774 (ppp) cc_final: 0.8450 (ppp) REVERT: B 567 ASN cc_start: 0.9577 (t0) cc_final: 0.9308 (m-40) REVERT: B 609 MET cc_start: 0.8910 (mmp) cc_final: 0.8576 (mmp) REVERT: B 646 MET cc_start: 0.9695 (mmp) cc_final: 0.9467 (mmm) REVERT: A 128 MET cc_start: 0.9373 (mtm) cc_final: 0.8927 (mtp) REVERT: A 174 PHE cc_start: 0.9563 (m-10) cc_final: 0.9337 (m-80) REVERT: A 235 PHE cc_start: 0.8628 (t80) cc_final: 0.7672 (t80) REVERT: A 311 PHE cc_start: 0.8595 (m-80) cc_final: 0.8281 (m-80) REVERT: A 399 PHE cc_start: 0.8825 (m-80) cc_final: 0.8305 (m-80) REVERT: A 410 MET cc_start: 0.9544 (tpt) cc_final: 0.9260 (tpp) REVERT: A 466 MET cc_start: 0.9322 (tpt) cc_final: 0.8944 (tpt) REVERT: A 470 MET cc_start: 0.8852 (ppp) cc_final: 0.8620 (ppp) REVERT: A 485 MET cc_start: 0.9565 (mmp) cc_final: 0.9288 (mmm) REVERT: A 488 PHE cc_start: 0.9279 (m-10) cc_final: 0.8980 (m-10) REVERT: A 559 MET cc_start: 0.9643 (ptm) cc_final: 0.9015 (ppp) REVERT: A 560 MET cc_start: 0.9681 (mtm) cc_final: 0.8728 (mpp) REVERT: A 609 MET cc_start: 0.8901 (mmp) cc_final: 0.8534 (mmp) REVERT: A 646 MET cc_start: 0.9637 (mmp) cc_final: 0.9380 (mmm) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1684 time to fit residues: 47.7748 Evaluate side-chains 145 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9467 Z= 0.210 Angle : 0.839 12.285 12861 Z= 0.420 Chirality : 0.046 0.187 1519 Planarity : 0.004 0.054 1573 Dihedral : 6.549 45.250 1260 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.62 (0.25), residues: 1177 helix: 1.03 (0.19), residues: 764 sheet: -2.34 (1.03), residues: 24 loop : -3.36 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 469 HIS 0.006 0.001 HIS B 451 PHE 0.030 0.002 PHE B 488 TYR 0.070 0.002 TYR B 589 ARG 0.002 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.986 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: B 128 MET cc_start: 0.9396 (mtm) cc_final: 0.9122 (mtt) REVERT: B 174 PHE cc_start: 0.9633 (m-10) cc_final: 0.9424 (m-80) REVERT: B 250 MET cc_start: 0.8759 (mmp) cc_final: 0.8476 (mmm) REVERT: B 267 LEU cc_start: 0.9738 (mp) cc_final: 0.9509 (tp) REVERT: B 307 PHE cc_start: 0.9445 (t80) cc_final: 0.8603 (t80) REVERT: B 339 MET cc_start: 0.8953 (ptp) cc_final: 0.8714 (ptp) REVERT: B 374 LEU cc_start: 0.9211 (tp) cc_final: 0.8985 (mt) REVERT: B 399 PHE cc_start: 0.9013 (m-80) cc_final: 0.8550 (m-80) REVERT: B 410 MET cc_start: 0.9572 (tpt) cc_final: 0.9271 (tpp) REVERT: B 414 MET cc_start: 0.9220 (tmm) cc_final: 0.8872 (tmm) REVERT: B 470 MET cc_start: 0.8827 (ppp) cc_final: 0.8555 (ppp) REVERT: B 559 MET cc_start: 0.9744 (ttt) cc_final: 0.9310 (tmm) REVERT: B 560 MET cc_start: 0.9350 (mpp) cc_final: 0.8645 (mpp) REVERT: B 567 ASN cc_start: 0.9578 (t0) cc_final: 0.9300 (m-40) REVERT: B 609 MET cc_start: 0.8527 (mmp) cc_final: 0.8260 (mmp) REVERT: B 646 MET cc_start: 0.9691 (mmp) cc_final: 0.9462 (mmm) REVERT: B 854 MET cc_start: 0.8668 (tmm) cc_final: 0.8445 (tmm) REVERT: A 128 MET cc_start: 0.9415 (mtm) cc_final: 0.8973 (mtp) REVERT: A 174 PHE cc_start: 0.9554 (m-10) cc_final: 0.9334 (m-80) REVERT: A 181 LEU cc_start: 0.8486 (mm) cc_final: 0.8149 (mt) REVERT: A 235 PHE cc_start: 0.8627 (t80) cc_final: 0.7700 (t80) REVERT: A 311 PHE cc_start: 0.8677 (m-80) cc_final: 0.8230 (m-80) REVERT: A 399 PHE cc_start: 0.8859 (m-80) cc_final: 0.8351 (m-80) REVERT: A 410 MET cc_start: 0.9550 (tpt) cc_final: 0.9244 (tpp) REVERT: A 414 MET cc_start: 0.9047 (tmm) cc_final: 0.8696 (tmm) REVERT: A 466 MET cc_start: 0.9221 (tpt) cc_final: 0.8901 (tpt) REVERT: A 470 MET cc_start: 0.8883 (ppp) cc_final: 0.8651 (ppp) REVERT: A 488 PHE cc_start: 0.9265 (m-10) cc_final: 0.8990 (m-10) REVERT: A 560 MET cc_start: 0.9594 (mtm) cc_final: 0.9299 (mtp) REVERT: A 609 MET cc_start: 0.8600 (mmp) cc_final: 0.8298 (mmp) REVERT: A 646 MET cc_start: 0.9637 (mmp) cc_final: 0.9381 (mmm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1650 time to fit residues: 46.3579 Evaluate side-chains 148 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9467 Z= 0.199 Angle : 0.847 11.904 12861 Z= 0.418 Chirality : 0.046 0.178 1519 Planarity : 0.004 0.049 1573 Dihedral : 6.278 37.112 1260 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.48 (0.25), residues: 1177 helix: 1.11 (0.19), residues: 767 sheet: -2.16 (1.05), residues: 24 loop : -3.30 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 469 HIS 0.011 0.001 HIS B 555 PHE 0.050 0.002 PHE B 488 TYR 0.056 0.002 TYR B 589 ARG 0.002 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9426 (mtm) cc_final: 0.9048 (mtp) REVERT: B 174 PHE cc_start: 0.9635 (m-10) cc_final: 0.9427 (m-80) REVERT: B 246 LEU cc_start: 0.9302 (tp) cc_final: 0.9098 (tp) REVERT: B 250 MET cc_start: 0.8748 (mmp) cc_final: 0.8471 (mmm) REVERT: B 267 LEU cc_start: 0.9752 (mp) cc_final: 0.9521 (tp) REVERT: B 311 PHE cc_start: 0.8738 (m-80) cc_final: 0.8271 (m-80) REVERT: B 373 MET cc_start: 0.8949 (mmp) cc_final: 0.8692 (mtp) REVERT: B 374 LEU cc_start: 0.9185 (tp) cc_final: 0.8942 (mt) REVERT: B 399 PHE cc_start: 0.9034 (m-80) cc_final: 0.8595 (m-80) REVERT: B 410 MET cc_start: 0.9545 (tpt) cc_final: 0.9188 (tpt) REVERT: B 414 MET cc_start: 0.9226 (tmm) cc_final: 0.8817 (tmm) REVERT: B 567 ASN cc_start: 0.9540 (t0) cc_final: 0.9234 (m-40) REVERT: B 609 MET cc_start: 0.8537 (mmp) cc_final: 0.8271 (mmp) REVERT: B 646 MET cc_start: 0.9687 (mmp) cc_final: 0.9453 (mmm) REVERT: B 868 LYS cc_start: 0.9640 (tmtt) cc_final: 0.9425 (tptp) REVERT: A 128 MET cc_start: 0.9401 (mtm) cc_final: 0.8974 (mtp) REVERT: A 174 PHE cc_start: 0.9544 (m-10) cc_final: 0.9322 (m-80) REVERT: A 181 LEU cc_start: 0.8540 (mm) cc_final: 0.8234 (mt) REVERT: A 311 PHE cc_start: 0.8732 (m-80) cc_final: 0.8258 (m-80) REVERT: A 399 PHE cc_start: 0.8856 (m-80) cc_final: 0.8382 (m-80) REVERT: A 410 MET cc_start: 0.9526 (tpt) cc_final: 0.9285 (tpp) REVERT: A 466 MET cc_start: 0.9198 (tpt) cc_final: 0.8881 (tpp) REVERT: A 609 MET cc_start: 0.8528 (mmp) cc_final: 0.8277 (mmp) REVERT: A 646 MET cc_start: 0.9632 (mmp) cc_final: 0.9370 (mmm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1683 time to fit residues: 47.4999 Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.0060 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 0.0270 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9467 Z= 0.198 Angle : 0.854 11.286 12861 Z= 0.418 Chirality : 0.047 0.180 1519 Planarity : 0.005 0.078 1573 Dihedral : 6.175 35.348 1260 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.38 (0.25), residues: 1177 helix: 1.19 (0.19), residues: 769 sheet: -2.04 (1.04), residues: 24 loop : -3.31 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 469 HIS 0.005 0.001 HIS B 555 PHE 0.052 0.002 PHE B 488 TYR 0.048 0.002 TYR B 589 ARG 0.002 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9414 (mtm) cc_final: 0.9070 (mtp) REVERT: B 174 PHE cc_start: 0.9626 (m-10) cc_final: 0.9412 (m-80) REVERT: B 246 LEU cc_start: 0.9288 (tp) cc_final: 0.9075 (tp) REVERT: B 250 MET cc_start: 0.8727 (mmp) cc_final: 0.8460 (mmm) REVERT: B 267 LEU cc_start: 0.9750 (mp) cc_final: 0.9515 (tp) REVERT: B 307 PHE cc_start: 0.9028 (t80) cc_final: 0.8378 (t80) REVERT: B 310 THR cc_start: 0.9641 (p) cc_final: 0.9425 (p) REVERT: B 311 PHE cc_start: 0.8755 (m-80) cc_final: 0.8339 (m-80) REVERT: B 319 LEU cc_start: 0.9661 (tp) cc_final: 0.9438 (tp) REVERT: B 339 MET cc_start: 0.9001 (ptm) cc_final: 0.8792 (ptp) REVERT: B 374 LEU cc_start: 0.9186 (tp) cc_final: 0.8964 (mt) REVERT: B 399 PHE cc_start: 0.9048 (m-80) cc_final: 0.8641 (m-80) REVERT: B 410 MET cc_start: 0.9519 (tpt) cc_final: 0.9153 (tpt) REVERT: B 414 MET cc_start: 0.9203 (tmm) cc_final: 0.8789 (tmm) REVERT: B 567 ASN cc_start: 0.9531 (t0) cc_final: 0.9226 (m-40) REVERT: B 609 MET cc_start: 0.8536 (mmp) cc_final: 0.8266 (mmp) REVERT: B 646 MET cc_start: 0.9670 (mmp) cc_final: 0.9419 (mmm) REVERT: A 128 MET cc_start: 0.9347 (mtm) cc_final: 0.9068 (mtp) REVERT: A 174 PHE cc_start: 0.9529 (m-10) cc_final: 0.9302 (m-80) REVERT: A 181 LEU cc_start: 0.8434 (mm) cc_final: 0.8224 (mm) REVERT: A 311 PHE cc_start: 0.8745 (m-80) cc_final: 0.8252 (m-80) REVERT: A 319 LEU cc_start: 0.9685 (tp) cc_final: 0.9478 (tp) REVERT: A 339 MET cc_start: 0.8907 (ptp) cc_final: 0.8648 (ptp) REVERT: A 399 PHE cc_start: 0.8835 (m-80) cc_final: 0.8369 (m-80) REVERT: A 404 PHE cc_start: 0.8788 (p90) cc_final: 0.8560 (p90) REVERT: A 410 MET cc_start: 0.9497 (tpt) cc_final: 0.9240 (tpp) REVERT: A 414 MET cc_start: 0.9023 (tmm) cc_final: 0.8616 (tmm) REVERT: A 560 MET cc_start: 0.9523 (mtm) cc_final: 0.9233 (mpp) REVERT: A 609 MET cc_start: 0.8612 (mmp) cc_final: 0.8307 (mmp) REVERT: A 646 MET cc_start: 0.9623 (mmp) cc_final: 0.9358 (mmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1784 time to fit residues: 51.3802 Evaluate side-chains 148 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9467 Z= 0.218 Angle : 0.862 11.136 12861 Z= 0.427 Chirality : 0.046 0.175 1519 Planarity : 0.005 0.062 1573 Dihedral : 6.112 32.561 1260 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.39 (0.25), residues: 1177 helix: 1.18 (0.19), residues: 770 sheet: -2.06 (1.02), residues: 24 loop : -3.29 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 469 HIS 0.007 0.001 HIS B 451 PHE 0.050 0.002 PHE B 488 TYR 0.046 0.002 TYR B 589 ARG 0.004 0.000 ARG A 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9473 (mtm) cc_final: 0.9009 (ptp) REVERT: B 174 PHE cc_start: 0.9621 (m-10) cc_final: 0.9416 (m-80) REVERT: B 246 LEU cc_start: 0.9311 (tp) cc_final: 0.9110 (tp) REVERT: B 250 MET cc_start: 0.8704 (mmp) cc_final: 0.8399 (mmm) REVERT: B 267 LEU cc_start: 0.9764 (mp) cc_final: 0.9542 (tp) REVERT: B 307 PHE cc_start: 0.9049 (t80) cc_final: 0.8355 (t80) REVERT: B 311 PHE cc_start: 0.8823 (m-80) cc_final: 0.8445 (m-80) REVERT: B 319 LEU cc_start: 0.9667 (tp) cc_final: 0.9453 (tp) REVERT: B 373 MET cc_start: 0.7745 (mtm) cc_final: 0.7477 (mtp) REVERT: B 399 PHE cc_start: 0.9034 (m-80) cc_final: 0.8640 (m-80) REVERT: B 410 MET cc_start: 0.9535 (tpt) cc_final: 0.9252 (tpp) REVERT: B 414 MET cc_start: 0.9186 (tmm) cc_final: 0.8950 (tmm) REVERT: B 470 MET cc_start: 0.8834 (ppp) cc_final: 0.8569 (ppp) REVERT: B 567 ASN cc_start: 0.9537 (t0) cc_final: 0.9231 (m-40) REVERT: B 609 MET cc_start: 0.8462 (mmp) cc_final: 0.8186 (mmp) REVERT: B 646 MET cc_start: 0.9675 (mmp) cc_final: 0.9432 (mmm) REVERT: A 128 MET cc_start: 0.9359 (mtm) cc_final: 0.8992 (mtp) REVERT: A 174 PHE cc_start: 0.9543 (m-10) cc_final: 0.9298 (m-80) REVERT: A 181 LEU cc_start: 0.8388 (mm) cc_final: 0.8166 (mm) REVERT: A 311 PHE cc_start: 0.8845 (m-80) cc_final: 0.8375 (m-80) REVERT: A 339 MET cc_start: 0.9046 (ptp) cc_final: 0.8697 (ptp) REVERT: A 399 PHE cc_start: 0.8818 (m-80) cc_final: 0.8335 (m-80) REVERT: A 410 MET cc_start: 0.9530 (tpt) cc_final: 0.9293 (tpp) REVERT: A 466 MET cc_start: 0.9265 (tpt) cc_final: 0.9060 (tpt) REVERT: A 559 MET cc_start: 0.9737 (ttt) cc_final: 0.9199 (ppp) REVERT: A 560 MET cc_start: 0.9567 (mtm) cc_final: 0.8750 (mtm) REVERT: A 609 MET cc_start: 0.8534 (mmp) cc_final: 0.8237 (mmp) REVERT: A 646 MET cc_start: 0.9623 (mmp) cc_final: 0.9366 (mmm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1742 time to fit residues: 48.6302 Evaluate side-chains 142 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 0.0470 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.063509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050765 restraints weight = 58025.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052271 restraints weight = 37990.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053202 restraints weight = 27583.862| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9467 Z= 0.197 Angle : 0.881 11.323 12861 Z= 0.428 Chirality : 0.047 0.179 1519 Planarity : 0.005 0.056 1573 Dihedral : 5.977 31.873 1260 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.30 (0.26), residues: 1177 helix: 1.25 (0.19), residues: 758 sheet: -1.85 (1.07), residues: 24 loop : -3.12 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 469 HIS 0.006 0.001 HIS B 555 PHE 0.051 0.002 PHE B 488 TYR 0.044 0.002 TYR B 589 ARG 0.002 0.000 ARG A 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.57 seconds wall clock time: 36 minutes 37.66 seconds (2197.66 seconds total)