Starting phenix.real_space_refine on Thu Feb 15 02:33:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poe_17789/02_2024/8poe_17789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poe_17789/02_2024/8poe_17789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poe_17789/02_2024/8poe_17789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poe_17789/02_2024/8poe_17789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poe_17789/02_2024/8poe_17789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poe_17789/02_2024/8poe_17789.pdb" } resolution = 4.2 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= 0.004 sd= 0.076 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 30 5.16 5 C 7185 2.51 5 N 1929 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 426": "OD1" <-> "OD2" Residue "C PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10947 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3649 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Chain: "B" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3649 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3649 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Time building chain proxies: 6.12, per 1000 atoms: 0.56 Number of scatterers: 10947 At special positions: 0 Unit cell: (130.68, 131.76, 89.64, 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 30 16.00 O 1803 8.00 N 1929 7.00 C 7185 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: 4.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 78.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.822A pdb=" N PHE A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 3.867A pdb=" N VAL A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.570A pdb=" N ALA A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 279 through 318 removed outlier: 3.651A pdb=" N ASP A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 353 through 375 removed outlier: 3.681A pdb=" N ILE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 427 through 470 Proline residue: A 451 - end of helix removed outlier: 3.630A pdb=" N LEU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.252A pdb=" N LEU A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 495 through 517 removed outlier: 4.871A pdb=" N ARG A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 3.578A pdb=" N ALA A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 548 removed outlier: 3.933A pdb=" N TYR A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 576 removed outlier: 3.676A pdb=" N ALA A 561 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.920A pdb=" N HIS A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 620 Processing helix chain 'A' and resid 622 through 645 Proline residue: A 634 - end of helix Proline residue: A 638 - end of helix removed outlier: 3.874A pdb=" N LEU A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.782A pdb=" N PHE B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 235 Processing helix chain 'B' and resid 237 through 243 removed outlier: 3.619A pdb=" N LEU B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 279 through 318 removed outlier: 3.603A pdb=" N ASP B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 353 through 374 removed outlier: 3.572A pdb=" N ILE B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THR B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 427 through 470 Proline residue: B 451 - end of helix removed outlier: 3.627A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 478 removed outlier: 4.285A pdb=" N LEU B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 495 through 517 removed outlier: 4.994A pdb=" N ARG B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Proline residue: B 509 - end of helix removed outlier: 3.648A pdb=" N ALA B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 548 removed outlier: 3.876A pdb=" N TYR B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 576 removed outlier: 3.643A pdb=" N ALA B 561 " --> pdb=" O HIS B 557 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 598 removed outlier: 4.092A pdb=" N HIS B 596 " --> pdb=" O THR B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 620 Processing helix chain 'B' and resid 622 through 645 Proline residue: B 634 - end of helix Proline residue: B 638 - end of helix removed outlier: 3.895A pdb=" N LEU B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 659 removed outlier: 3.527A pdb=" N ILE B 653 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 205 removed outlier: 3.796A pdb=" N PHE C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 235 Processing helix chain 'C' and resid 237 through 243 removed outlier: 3.625A pdb=" N LEU C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 279 through 318 removed outlier: 3.512A pdb=" N LEU C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 329 through 342 Processing helix chain 'C' and resid 353 through 374 removed outlier: 3.551A pdb=" N ILE C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TYR C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 427 through 470 Proline residue: C 451 - end of helix removed outlier: 3.617A pdb=" N LEU C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 477 removed outlier: 4.197A pdb=" N LEU C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 489 Processing helix chain 'C' and resid 495 through 517 removed outlier: 5.026A pdb=" N ARG C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Proline residue: C 509 - end of helix removed outlier: 3.526A pdb=" N ALA C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 548 removed outlier: 3.955A pdb=" N TYR C 548 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 576 removed outlier: 3.739A pdb=" N ALA C 561 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 564 " --> pdb=" O THR C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 598 removed outlier: 3.977A pdb=" N HIS C 596 " --> pdb=" O THR C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 620 Processing helix chain 'C' and resid 622 through 645 Proline residue: C 634 - end of helix Proline residue: C 638 - end of helix removed outlier: 3.908A pdb=" N LEU C 641 " --> pdb=" O THR C 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 659 removed outlier: 3.500A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 660 through 663 Processing sheet with id=AA2, first strand: chain 'B' and resid 660 through 663 Processing sheet with id=AA3, first strand: chain 'C' and resid 660 through 663 741 hydrogen bonds defined for protein. 2172 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: 2.72 Time building geometry restraints manager: 5.07 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: 3506 1.34 - 1.46: 2581 1.46 - 1.58: 5109 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 11235 Sorted by residual: bond pdb=" C LEU B 377 " pdb=" N PRO B 378 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.45e+00 bond pdb=" CG1 ILE B 225 " pdb=" CD1 ILE B 225 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CG1 ILE C 225 " pdb=" CD1 ILE C 225 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.49e+00 bond pdb=" CG GLN A 221 " pdb=" CD GLN A 221 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.66e-02 3.63e+03 1.01e+00 ... (remaining 11230 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.09: 374 107.09 - 113.83: 6214 113.83 - 120.56: 4809 120.56 - 127.30: 3755 127.30 - 134.03: 154 Bond angle restraints: 15306 Sorted by residual: angle pdb=" N GLU C 273 " pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " ideal model delta sigma weight residual 110.28 116.14 -5.86 1.55e+00 4.16e-01 1.43e+01 angle pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " pdb=" CG GLU C 273 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N GLU A 273 " pdb=" CA GLU A 273 " pdb=" CB GLU A 273 " ideal model delta sigma weight residual 110.12 115.10 -4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" N GLU B 273 " pdb=" CA GLU B 273 " pdb=" CB GLU B 273 " ideal model delta sigma weight residual 110.12 114.94 -4.82 1.47e+00 4.63e-01 1.07e+01 angle pdb=" N GLN C 340 " pdb=" CA GLN C 340 " pdb=" CB GLN C 340 " ideal model delta sigma weight residual 110.28 115.36 -5.08 1.55e+00 4.16e-01 1.07e+01 ... (remaining 15301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5959 17.71 - 35.43: 501 35.43 - 53.14: 113 53.14 - 70.85: 18 70.85 - 88.56: 9 Dihedral angle restraints: 6600 sinusoidal: 2598 harmonic: 4002 Sorted by residual: dihedral pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " pdb=" CG ASP A 215 " pdb=" OD1 ASP A 215 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU C 417 " pdb=" CG GLU C 417 " pdb=" CD GLU C 417 " pdb=" OE1 GLU C 417 " ideal model delta sinusoidal sigma weight residual 0.00 -88.56 88.56 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU C 376 " pdb=" C LEU C 376 " pdb=" N LEU C 377 " pdb=" CA LEU C 377 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1114 0.032 - 0.064: 460 0.064 - 0.096: 122 0.096 - 0.128: 56 0.128 - 0.159: 9 Chirality restraints: 1761 Sorted by residual: chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASN A 206 " pdb=" N ASN A 206 " pdb=" C ASN A 206 " pdb=" CB ASN A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CG LEU B 362 " pdb=" CB LEU B 362 " pdb=" CD1 LEU B 362 " pdb=" CD2 LEU B 362 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1758 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 533 " 0.021 2.00e-02 2.50e+03 1.86e-02 6.04e+00 pdb=" CG PHE B 533 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 533 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 533 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 533 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 533 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 533 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 508 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 509 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 533 " -0.018 2.00e-02 2.50e+03 1.22e-02 2.61e+00 pdb=" CG PHE A 533 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 533 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 533 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 533 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 533 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 533 " -0.009 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2471 2.79 - 3.32: 11000 3.32 - 3.85: 17505 3.85 - 4.37: 17764 4.37 - 4.90: 30949 Nonbonded interactions: 79689 Sorted by model distance: nonbonded pdb=" NH1 ARG B 363 " pdb=" OD1 ASP B 668 " model vdw 2.265 2.520 nonbonded pdb=" NH1 ARG C 363 " pdb=" OD1 ASP C 668 " model vdw 2.273 2.520 nonbonded pdb=" OD1 ASN C 399 " pdb=" ND2 ASN C 446 " model vdw 2.287 2.520 nonbonded pdb=" O ARG B 276 " pdb=" NH1 ARG B 276 " model vdw 2.289 2.520 nonbonded pdb=" N GLU A 354 " pdb=" OE1 GLU A 354 " model vdw 2.297 2.520 ... (remaining 79684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.020 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: 5.200 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.450 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.003 0.049 11235 Z= 0.172 Angle : 0.637 9.178 15306 Z= 0.331 Chirality : 0.040 0.159 1761 Planarity : 0.004 0.041 1926 Dihedral : 14.198 88.563 3996 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1341 helix: 1.65 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 435 HIS 0.005 0.001 HIS B 497 PHE 0.042 0.001 PHE B 533 TYR 0.012 0.001 TYR A 622 ARG 0.005 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 TYR cc_start: 0.7571 (t80) cc_final: 0.7234 (t80) REVERT: A 562 MET cc_start: 0.7838 (mmm) cc_final: 0.7518 (mmt) REVERT: A 630 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 669 ILE cc_start: 0.7986 (mt) cc_final: 0.7783 (mt) REVERT: B 219 LEU cc_start: 0.9006 (mt) cc_final: 0.8785 (mt) REVERT: B 494 GLU cc_start: 0.8289 (tp30) cc_final: 0.8000 (tp30) REVERT: B 669 ILE cc_start: 0.8167 (mt) cc_final: 0.7950 (mt) REVERT: C 356 ASP cc_start: 0.7617 (m-30) cc_final: 0.7280 (m-30) REVERT: C 669 ILE cc_start: 0.7701 (mt) cc_final: 0.7387 (mt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2229 time to fit residues: 89.2190 Evaluate side-chains 210 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 0.0020 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 446 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS B 530 GLN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11235 Z= 0.154 Angle : 0.541 5.956 15306 Z= 0.273 Chirality : 0.038 0.158 1761 Planarity : 0.004 0.039 1926 Dihedral : 3.585 15.387 1515 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.26 % Allowed : 5.28 % Favored : 94.46 % 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: 1.50 (0.24), residues: 1341 helix: 1.73 (0.17), residues: 969 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 329 HIS 0.004 0.001 HIS B 497 PHE 0.028 0.001 PHE B 533 TYR 0.013 0.001 TYR C 622 ARG 0.003 0.000 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 292 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 TYR cc_start: 0.7570 (t80) cc_final: 0.7280 (t80) REVERT: A 562 MET cc_start: 0.7943 (mmm) cc_final: 0.7667 (mmt) REVERT: A 630 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 669 ILE cc_start: 0.7926 (mt) cc_final: 0.7624 (mt) REVERT: B 219 LEU cc_start: 0.9033 (mt) cc_final: 0.8800 (mt) REVERT: B 362 LEU cc_start: 0.8604 (mm) cc_final: 0.8214 (mm) REVERT: B 494 GLU cc_start: 0.8280 (tp30) cc_final: 0.7993 (tp30) REVERT: B 669 ILE cc_start: 0.8151 (mt) cc_final: 0.7877 (mt) REVERT: C 356 ASP cc_start: 0.7611 (m-30) cc_final: 0.7377 (m-30) REVERT: C 630 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8337 (mm-30) REVERT: C 669 ILE cc_start: 0.7780 (mt) cc_final: 0.7420 (mt) outliers start: 3 outliers final: 1 residues processed: 293 average time/residue: 0.1927 time to fit residues: 78.9501 Evaluate side-chains 217 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 0.0050 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 598 HIS ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS C 399 ASN C 446 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11235 Z= 0.165 Angle : 0.548 5.677 15306 Z= 0.276 Chirality : 0.039 0.167 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.559 15.832 1515 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.22 % 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: 1.51 (0.24), residues: 1341 helix: 1.79 (0.16), residues: 981 sheet: None (None), residues: 0 loop : -1.22 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 644 HIS 0.005 0.001 HIS B 203 PHE 0.030 0.001 PHE B 533 TYR 0.018 0.001 TYR B 306 ARG 0.004 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 302 time to evaluate : 1.155 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: A 548 TYR cc_start: 0.7521 (t80) cc_final: 0.7257 (t80) REVERT: A 669 ILE cc_start: 0.7906 (mt) cc_final: 0.7572 (mt) REVERT: B 356 ASP cc_start: 0.8124 (m-30) cc_final: 0.7873 (m-30) REVERT: B 362 LEU cc_start: 0.8648 (mm) cc_final: 0.8251 (mm) REVERT: B 494 GLU cc_start: 0.8205 (tp30) cc_final: 0.7987 (tp30) REVERT: B 669 ILE cc_start: 0.8133 (mt) cc_final: 0.7888 (mt) REVERT: C 356 ASP cc_start: 0.7798 (m-30) cc_final: 0.7563 (m-30) REVERT: C 669 ILE cc_start: 0.8125 (mt) cc_final: 0.7826 (mt) outliers start: 2 outliers final: 0 residues processed: 302 average time/residue: 0.2161 time to fit residues: 90.0566 Evaluate side-chains 213 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11235 Z= 0.152 Angle : 0.540 6.006 15306 Z= 0.269 Chirality : 0.039 0.161 1761 Planarity : 0.004 0.037 1926 Dihedral : 3.533 14.916 1515 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % 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: 1.54 (0.23), residues: 1341 helix: 1.78 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -1.05 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.003 0.001 HIS B 497 PHE 0.029 0.001 PHE B 533 TYR 0.012 0.001 TYR B 622 ARG 0.003 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 CYS cc_start: 0.7823 (t) cc_final: 0.7600 (m) REVERT: A 548 TYR cc_start: 0.7480 (t80) cc_final: 0.7257 (t80) REVERT: A 669 ILE cc_start: 0.7879 (mt) cc_final: 0.7542 (mt) REVERT: B 356 ASP cc_start: 0.8045 (m-30) cc_final: 0.7794 (m-30) REVERT: B 362 LEU cc_start: 0.8668 (mm) cc_final: 0.8296 (mm) REVERT: B 659 PHE cc_start: 0.7608 (m-80) cc_final: 0.7325 (m-80) REVERT: B 669 ILE cc_start: 0.7961 (mt) cc_final: 0.7730 (mt) REVERT: C 356 ASP cc_start: 0.7892 (m-30) cc_final: 0.7613 (m-30) REVERT: C 669 ILE cc_start: 0.8090 (mt) cc_final: 0.7804 (mt) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.2326 time to fit residues: 94.4361 Evaluate side-chains 212 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.0270 chunk 117 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11235 Z= 0.144 Angle : 0.548 6.215 15306 Z= 0.272 Chirality : 0.038 0.158 1761 Planarity : 0.004 0.037 1926 Dihedral : 3.511 14.511 1515 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % Rotamer: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % 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: 1.57 (0.23), residues: 1341 helix: 1.81 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 329 HIS 0.004 0.000 HIS B 497 PHE 0.029 0.001 PHE B 533 TYR 0.011 0.001 TYR A 622 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 1.230 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: A 235 CYS cc_start: 0.7867 (t) cc_final: 0.7661 (m) REVERT: A 548 TYR cc_start: 0.7488 (t80) cc_final: 0.7258 (t80) REVERT: A 669 ILE cc_start: 0.7857 (mt) cc_final: 0.7518 (mt) REVERT: B 219 LEU cc_start: 0.9003 (mt) cc_final: 0.8767 (mt) REVERT: B 362 LEU cc_start: 0.8595 (mm) cc_final: 0.8242 (mm) REVERT: B 669 ILE cc_start: 0.8088 (mt) cc_final: 0.7852 (mt) REVERT: C 356 ASP cc_start: 0.7733 (m-30) cc_final: 0.7518 (m-30) REVERT: C 393 SER cc_start: 0.8640 (t) cc_final: 0.8436 (t) REVERT: C 669 ILE cc_start: 0.8021 (mt) cc_final: 0.7748 (mt) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.2116 time to fit residues: 89.0124 Evaluate side-chains 222 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 491 HIS A 598 HIS B 333 GLN B 366 ASN C 491 HIS C 657 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11235 Z= 0.259 Angle : 0.660 7.446 15306 Z= 0.340 Chirality : 0.043 0.168 1761 Planarity : 0.005 0.036 1926 Dihedral : 3.883 19.460 1515 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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 (0.23), residues: 1341 helix: 1.47 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 385 HIS 0.004 0.001 HIS B 596 PHE 0.033 0.002 PHE B 533 TYR 0.035 0.002 TYR A 367 ARG 0.011 0.001 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 TYR cc_start: 0.7715 (t80) cc_final: 0.7461 (t80) REVERT: A 669 ILE cc_start: 0.7981 (mt) cc_final: 0.7609 (mt) REVERT: B 333 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6635 (tp40) REVERT: B 494 GLU cc_start: 0.8236 (tp30) cc_final: 0.8012 (tp30) REVERT: B 669 ILE cc_start: 0.8120 (mt) cc_final: 0.7877 (mt) REVERT: C 356 ASP cc_start: 0.7651 (m-30) cc_final: 0.7364 (m-30) REVERT: C 669 ILE cc_start: 0.8106 (mt) cc_final: 0.7868 (mt) REVERT: C 671 SER cc_start: 0.8928 (m) cc_final: 0.8674 (t) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2019 time to fit residues: 85.0166 Evaluate side-chains 209 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 HIS B 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11235 Z= 0.173 Angle : 0.589 6.679 15306 Z= 0.299 Chirality : 0.040 0.159 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.839 23.092 1515 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 1.21 (0.23), residues: 1341 helix: 1.50 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 329 HIS 0.003 0.001 HIS A 491 PHE 0.034 0.001 PHE B 533 TYR 0.017 0.001 TYR C 313 ARG 0.008 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.069 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: A 548 TYR cc_start: 0.7714 (t80) cc_final: 0.7454 (t80) REVERT: A 598 HIS cc_start: 0.7920 (m170) cc_final: 0.7719 (m-70) REVERT: A 630 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 669 ILE cc_start: 0.7889 (mt) cc_final: 0.7534 (mt) REVERT: B 333 GLN cc_start: 0.6762 (mm-40) cc_final: 0.6507 (tp40) REVERT: B 356 ASP cc_start: 0.8152 (m-30) cc_final: 0.7897 (m-30) REVERT: B 362 LEU cc_start: 0.8793 (mm) cc_final: 0.8470 (mm) REVERT: B 470 ARG cc_start: 0.7314 (tmm160) cc_final: 0.7071 (tmm160) REVERT: B 669 ILE cc_start: 0.8066 (mt) cc_final: 0.7838 (mt) REVERT: C 630 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8302 (mm-30) REVERT: C 669 ILE cc_start: 0.8139 (mt) cc_final: 0.7872 (mt) REVERT: C 671 SER cc_start: 0.8889 (m) cc_final: 0.8644 (t) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1815 time to fit residues: 73.2516 Evaluate side-chains 209 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 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 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11235 Z= 0.163 Angle : 0.566 6.590 15306 Z= 0.286 Chirality : 0.039 0.166 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.692 15.966 1515 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.09 % Allowed : 1.93 % Favored : 97.98 % 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: 1.33 (0.23), residues: 1341 helix: 1.61 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.09 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 644 HIS 0.003 0.001 HIS A 491 PHE 0.034 0.001 PHE B 533 TYR 0.011 0.001 TYR B 622 ARG 0.006 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 1.157 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: A 263 ASP cc_start: 0.8676 (m-30) cc_final: 0.8475 (m-30) REVERT: A 548 TYR cc_start: 0.7673 (t80) cc_final: 0.7457 (t80) REVERT: A 598 HIS cc_start: 0.7922 (m170) cc_final: 0.7699 (m90) REVERT: A 669 ILE cc_start: 0.7855 (mt) cc_final: 0.7492 (mt) REVERT: B 263 ASP cc_start: 0.8724 (m-30) cc_final: 0.8492 (m-30) REVERT: B 362 LEU cc_start: 0.8798 (mm) cc_final: 0.8426 (mm) REVERT: B 659 PHE cc_start: 0.7531 (m-80) cc_final: 0.7228 (m-80) REVERT: B 669 ILE cc_start: 0.8110 (mt) cc_final: 0.7822 (mt) REVERT: C 356 ASP cc_start: 0.7878 (m-30) cc_final: 0.7650 (m-30) REVERT: C 669 ILE cc_start: 0.8139 (mt) cc_final: 0.7892 (mt) REVERT: C 671 SER cc_start: 0.8830 (m) cc_final: 0.8564 (t) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.1921 time to fit residues: 76.8373 Evaluate side-chains 212 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.0370 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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: 0.7147 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11235 Z= 0.165 Angle : 0.583 6.624 15306 Z= 0.292 Chirality : 0.039 0.161 1761 Planarity : 0.004 0.037 1926 Dihedral : 3.645 15.849 1515 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 1.39 (0.24), residues: 1341 helix: 1.67 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -1.09 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 644 HIS 0.003 0.000 HIS B 491 PHE 0.031 0.001 PHE B 533 TYR 0.015 0.001 TYR C 313 ARG 0.006 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8680 (m-30) cc_final: 0.8474 (m-30) REVERT: A 669 ILE cc_start: 0.7848 (mt) cc_final: 0.7488 (mt) REVERT: B 263 ASP cc_start: 0.8752 (m-30) cc_final: 0.8533 (m-30) REVERT: B 356 ASP cc_start: 0.8133 (m-30) cc_final: 0.7817 (m-30) REVERT: B 362 LEU cc_start: 0.8810 (mm) cc_final: 0.8507 (mm) REVERT: B 470 ARG cc_start: 0.7318 (tmm160) cc_final: 0.7094 (tmm160) REVERT: B 669 ILE cc_start: 0.8085 (mt) cc_final: 0.7807 (mt) REVERT: C 356 ASP cc_start: 0.7860 (m-30) cc_final: 0.7608 (m-30) REVERT: C 423 LYS cc_start: 0.7331 (tppt) cc_final: 0.7099 (tppp) REVERT: C 669 ILE cc_start: 0.8189 (mt) cc_final: 0.7921 (mt) REVERT: C 671 SER cc_start: 0.8820 (m) cc_final: 0.8529 (t) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1873 time to fit residues: 75.4074 Evaluate side-chains 217 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 134 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11235 Z= 0.164 Angle : 0.590 7.003 15306 Z= 0.298 Chirality : 0.039 0.160 1761 Planarity : 0.004 0.037 1926 Dihedral : 3.649 16.180 1515 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.09 % Allowed : 0.79 % Favored : 99.12 % 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: 1.41 (0.24), residues: 1341 helix: 1.65 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 644 HIS 0.005 0.001 HIS B 491 PHE 0.030 0.001 PHE B 533 TYR 0.015 0.001 TYR C 599 ARG 0.009 0.000 ARG C 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 0.922 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: A 263 ASP cc_start: 0.8672 (m-30) cc_final: 0.8467 (m-30) REVERT: A 669 ILE cc_start: 0.7878 (mt) cc_final: 0.7515 (mt) REVERT: B 263 ASP cc_start: 0.8751 (m-30) cc_final: 0.8529 (m-30) REVERT: B 333 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6961 (tp40) REVERT: B 356 ASP cc_start: 0.8129 (m-30) cc_final: 0.7833 (m-30) REVERT: B 362 LEU cc_start: 0.8827 (mm) cc_final: 0.8514 (mm) REVERT: B 659 PHE cc_start: 0.7692 (m-80) cc_final: 0.7289 (m-80) REVERT: B 669 ILE cc_start: 0.8068 (mt) cc_final: 0.7786 (mt) REVERT: C 219 LEU cc_start: 0.9018 (mt) cc_final: 0.8814 (mt) REVERT: C 356 ASP cc_start: 0.7880 (m-30) cc_final: 0.7654 (m-30) REVERT: C 423 LYS cc_start: 0.7428 (tppt) cc_final: 0.7178 (tppp) REVERT: C 669 ILE cc_start: 0.8166 (mt) cc_final: 0.7910 (mt) REVERT: C 671 SER cc_start: 0.8820 (m) cc_final: 0.8520 (t) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.1730 time to fit residues: 67.3913 Evaluate side-chains 212 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 0.0870 chunk 44 optimal weight: 0.0870 chunk 110 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: