Starting phenix.real_space_refine on Sat Nov 16 15:49:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/11_2024/8jpj_36481.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/11_2024/8jpj_36481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/11_2024/8jpj_36481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/11_2024/8jpj_36481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/11_2024/8jpj_36481.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/11_2024/8jpj_36481.cif" } resolution = 3.5 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= 0.005 sd= 0.070 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: 5 Type Number sf(0) Gaussians S 70 5.16 5 Cl 4 4.86 5 C 7436 2.51 5 N 1914 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5722 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 11.89, per 1000 atoms: 1.04 Number of scatterers: 11448 At special positions: 0 Unit cell: (106.35, 82.9026, 116.399, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 70 16.00 O 2024 8.00 N 1914 7.00 C 7436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 65.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 69 through 124 removed outlier: 3.646A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 151 removed outlier: 3.932A pdb=" N LEU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.077A pdb=" N CYS A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.882A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 removed outlier: 4.239A pdb=" N HIS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.591A pdb=" N GLN A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 276 through 299 removed outlier: 3.850A pdb=" N PHE A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 333 through 365 Processing helix chain 'A' and resid 375 through 395 removed outlier: 3.570A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 444 removed outlier: 3.553A pdb=" N ASN A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 488 through 511 removed outlier: 3.945A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.135A pdb=" N ALA A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.654A pdb=" N ILE A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.679A pdb=" N LEU A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.788A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 773 through 780 removed outlier: 4.288A pdb=" N ASP A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 830 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 69 through 124 removed outlier: 3.647A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 151 removed outlier: 3.933A pdb=" N LEU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.077A pdb=" N CYS B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.882A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 218 removed outlier: 4.239A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Proline residue: B 215 - end of helix removed outlier: 3.591A pdb=" N GLN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.851A pdb=" N PHE B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 333 through 365 Processing helix chain 'B' and resid 375 through 395 removed outlier: 3.571A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 444 removed outlier: 3.552A pdb=" N ASN B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'B' and resid 461 through 480 Processing helix chain 'B' and resid 488 through 511 removed outlier: 3.946A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 534 removed outlier: 4.134A pdb=" N ALA B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.655A pdb=" N ILE B 557 " --> pdb=" O TYR B 553 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 560 " --> pdb=" O PRO B 556 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 582 Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.679A pdb=" N LEU B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.789A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 773 through 780 removed outlier: 4.288A pdb=" N ASP B 780 " --> pdb=" O GLU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 830 Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 854 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.482A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838 Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 401 Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.482A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838 670 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3613 1.34 - 1.46: 2834 1.46 - 1.58: 5151 1.58 - 1.70: 0 1.70 - 1.82: 110 Bond restraints: 11708 Sorted by residual: bond pdb=" CA VAL A 758 " pdb=" CB VAL A 758 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.35e+00 bond pdb=" CA VAL B 758 " pdb=" CB VAL B 758 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.28e+00 bond pdb=" N PRO B 368 " pdb=" CA PRO B 368 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.21e+00 bond pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.51e-01 bond pdb=" CA ILE B 159 " pdb=" C ILE B 159 " ideal model delta sigma weight residual 1.520 1.528 -0.008 8.80e-03 1.29e+04 8.53e-01 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 15457 1.52 - 3.04: 337 3.04 - 4.57: 61 4.57 - 6.09: 21 6.09 - 7.61: 2 Bond angle restraints: 15878 Sorted by residual: angle pdb=" N VAL B 375 " pdb=" CA VAL B 375 " pdb=" C VAL B 375 " ideal model delta sigma weight residual 112.96 107.81 5.15 1.00e+00 1.00e+00 2.65e+01 angle pdb=" N VAL A 375 " pdb=" CA VAL A 375 " pdb=" C VAL A 375 " ideal model delta sigma weight residual 112.96 107.83 5.13 1.00e+00 1.00e+00 2.64e+01 angle pdb=" N VAL B 175 " pdb=" CA VAL B 175 " pdb=" C VAL B 175 " ideal model delta sigma weight residual 113.71 109.48 4.23 9.50e-01 1.11e+00 1.99e+01 angle pdb=" N VAL A 175 " pdb=" CA VAL A 175 " pdb=" C VAL A 175 " ideal model delta sigma weight residual 113.71 109.55 4.16 9.50e-01 1.11e+00 1.92e+01 angle pdb=" C GLY A 158 " pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 120.24 122.83 -2.59 6.30e-01 2.52e+00 1.69e+01 ... (remaining 15873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6249 17.54 - 35.08: 519 35.08 - 52.61: 96 52.61 - 70.15: 11 70.15 - 87.69: 12 Dihedral angle restraints: 6887 sinusoidal: 2689 harmonic: 4198 Sorted by residual: dihedral pdb=" CB CYS A 399 " pdb=" SG CYS A 399 " pdb=" SG CYS A 430 " pdb=" CB CYS A 430 " ideal model delta sinusoidal sigma weight residual 93.00 -179.31 -87.69 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual -86.00 -159.98 73.98 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CA VAL A 171 " pdb=" C VAL A 171 " pdb=" N PRO A 172 " pdb=" CA PRO A 172 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1144 0.029 - 0.058: 452 0.058 - 0.088: 139 0.088 - 0.117: 83 0.117 - 0.146: 16 Chirality restraints: 1834 Sorted by residual: chirality pdb=" CB THR A 427 " pdb=" CA THR A 427 " pdb=" OG1 THR A 427 " pdb=" CG2 THR A 427 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CB THR B 427 " pdb=" CA THR B 427 " pdb=" OG1 THR B 427 " pdb=" CG2 THR B 427 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE A 847 " pdb=" N ILE A 847 " pdb=" C ILE A 847 " pdb=" CB ILE A 847 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1831 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 369 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 370 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 369 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO A 370 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 769 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 770 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 770 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 770 " -0.021 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 51 2.60 - 3.18: 10073 3.18 - 3.75: 16796 3.75 - 4.33: 22487 4.33 - 4.90: 38539 Nonbonded interactions: 87946 Sorted by model distance: nonbonded pdb=" SG CYS B 120 " pdb=" SG CYS B 125 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 399 " pdb=" SG CYS B 430 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 319 " pdb=" SG CYS B 326 " model vdw 2.033 3.760 nonbonded pdb=" ND2 ASN B 137 " pdb=" OG1 THR B 386 " model vdw 2.279 3.120 nonbonded pdb=" ND2 ASN A 137 " pdb=" OG1 THR A 386 " model vdw 2.279 3.120 ... (remaining 87941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.680 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.840 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 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 0.025 11708 Z= 0.210 Angle : 0.575 7.608 15878 Z= 0.325 Chirality : 0.039 0.146 1834 Planarity : 0.004 0.037 1994 Dihedral : 13.482 83.984 4182 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 (0.23), residues: 1446 helix: 2.20 (0.18), residues: 892 sheet: -1.52 (1.08), residues: 24 loop : -1.08 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 303 HIS 0.002 0.000 HIS A 515 PHE 0.012 0.001 PHE B 101 TYR 0.012 0.001 TYR A 866 ARG 0.003 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6371 (pt0) REVERT: A 71 LYS cc_start: 0.5897 (mmtt) cc_final: 0.5676 (mttp) REVERT: A 75 ARG cc_start: 0.6007 (ttt90) cc_final: 0.5357 (tpt170) REVERT: A 82 MET cc_start: 0.6724 (mtt) cc_final: 0.6399 (mtt) REVERT: A 200 GLU cc_start: 0.6712 (mp0) cc_final: 0.5364 (mp0) REVERT: A 589 GLU cc_start: 0.6415 (pt0) cc_final: 0.5722 (pm20) REVERT: A 611 TYR cc_start: 0.6042 (p90) cc_final: 0.5560 (p90) REVERT: A 822 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6335 (mt0) REVERT: A 843 GLU cc_start: 0.5157 (tt0) cc_final: 0.4747 (tm-30) REVERT: A 844 ILE cc_start: 0.6251 (tt) cc_final: 0.5831 (tt) REVERT: A 855 TYR cc_start: 0.7427 (t80) cc_final: 0.6911 (t80) REVERT: B 63 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6370 (pt0) REVERT: B 71 LYS cc_start: 0.5899 (mmtt) cc_final: 0.5676 (mttp) REVERT: B 75 ARG cc_start: 0.6013 (ttt90) cc_final: 0.5360 (tpt170) REVERT: B 82 MET cc_start: 0.6721 (mtt) cc_final: 0.6394 (mtt) REVERT: B 200 GLU cc_start: 0.6696 (mp0) cc_final: 0.5348 (mp0) REVERT: B 589 GLU cc_start: 0.6405 (pt0) cc_final: 0.5716 (pm20) REVERT: B 611 TYR cc_start: 0.6094 (p90) cc_final: 0.5605 (p90) REVERT: B 822 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6337 (mt0) REVERT: B 843 GLU cc_start: 0.5203 (tt0) cc_final: 0.4748 (tm-30) REVERT: B 844 ILE cc_start: 0.6289 (tt) cc_final: 0.5874 (tt) REVERT: B 855 TYR cc_start: 0.7431 (t80) cc_final: 0.6885 (t80) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.3087 time to fit residues: 136.7925 Evaluate side-chains 168 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 355 ASN A 819 HIS A 859 GLN B 167 ASN B 819 HIS B 852 ASN B 859 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11708 Z= 0.258 Angle : 0.668 9.146 15878 Z= 0.343 Chirality : 0.044 0.149 1834 Planarity : 0.005 0.046 1994 Dihedral : 4.507 20.582 1574 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.31 % Allowed : 11.94 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1446 helix: 1.79 (0.17), residues: 908 sheet: -3.02 (0.87), residues: 24 loop : -0.83 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 272 HIS 0.008 0.001 HIS A 865 PHE 0.030 0.002 PHE A 473 TYR 0.019 0.002 TYR B 855 ARG 0.008 0.001 ARG B 861 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6305 (pt0) REVERT: A 71 LYS cc_start: 0.5995 (mttt) cc_final: 0.5730 (mttp) REVERT: A 82 MET cc_start: 0.7039 (mtt) cc_final: 0.6674 (mtt) REVERT: A 161 GLU cc_start: 0.6691 (mp0) cc_final: 0.5996 (mp0) REVERT: A 203 MET cc_start: 0.7586 (mmm) cc_final: 0.7385 (tpp) REVERT: A 239 ARG cc_start: 0.7156 (ttt-90) cc_final: 0.6864 (ttt180) REVERT: A 313 ASN cc_start: 0.7798 (p0) cc_final: 0.7463 (p0) REVERT: A 360 LYS cc_start: 0.6469 (mttt) cc_final: 0.6170 (mtmt) REVERT: A 361 TYR cc_start: 0.7743 (t80) cc_final: 0.7543 (t80) REVERT: A 573 LYS cc_start: 0.7662 (mttt) cc_final: 0.6423 (mmtm) REVERT: A 587 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7330 (mp) REVERT: A 589 GLU cc_start: 0.6349 (pt0) cc_final: 0.5699 (pm20) REVERT: A 822 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6398 (mt0) REVERT: B 63 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6308 (pt0) REVERT: B 71 LYS cc_start: 0.5996 (mttt) cc_final: 0.5732 (mttp) REVERT: B 82 MET cc_start: 0.7035 (mtt) cc_final: 0.6673 (mtt) REVERT: B 161 GLU cc_start: 0.6689 (mp0) cc_final: 0.5991 (mp0) REVERT: B 239 ARG cc_start: 0.7160 (ttt-90) cc_final: 0.6871 (ttt180) REVERT: B 313 ASN cc_start: 0.7789 (p0) cc_final: 0.7459 (p0) REVERT: B 360 LYS cc_start: 0.6462 (mttt) cc_final: 0.6162 (mtmt) REVERT: B 573 LYS cc_start: 0.7668 (mttt) cc_final: 0.6429 (mmtm) REVERT: B 587 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7325 (mp) REVERT: B 589 GLU cc_start: 0.6341 (pt0) cc_final: 0.5685 (pm20) REVERT: B 822 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6393 (mt0) outliers start: 29 outliers final: 8 residues processed: 194 average time/residue: 0.2903 time to fit residues: 77.0758 Evaluate side-chains 160 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 110 optimal weight: 0.2980 chunk 90 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN B 355 ASN B 456 GLN B 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11708 Z= 0.157 Angle : 0.525 12.839 15878 Z= 0.264 Chirality : 0.038 0.141 1834 Planarity : 0.004 0.037 1994 Dihedral : 4.029 19.013 1574 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.51 % Allowed : 12.74 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.22), residues: 1446 helix: 2.23 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 278 HIS 0.007 0.001 HIS A 865 PHE 0.017 0.001 PHE A 473 TYR 0.013 0.001 TYR B 613 ARG 0.003 0.000 ARG B 861 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6323 (pt0) REVERT: A 71 LYS cc_start: 0.5926 (mttt) cc_final: 0.5723 (mttp) REVERT: A 82 MET cc_start: 0.7094 (mtt) cc_final: 0.6719 (mtt) REVERT: A 119 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.5013 (mp0) REVERT: A 161 GLU cc_start: 0.6947 (mp0) cc_final: 0.5876 (mp0) REVERT: A 239 ARG cc_start: 0.7115 (ttt-90) cc_final: 0.6901 (ttt180) REVERT: A 313 ASN cc_start: 0.7816 (p0) cc_final: 0.7525 (p0) REVERT: A 360 LYS cc_start: 0.6480 (mttt) cc_final: 0.6064 (mtmm) REVERT: A 361 TYR cc_start: 0.7795 (t80) cc_final: 0.7540 (t80) REVERT: A 573 LYS cc_start: 0.7684 (mttt) cc_final: 0.7013 (mtmm) REVERT: A 587 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 589 GLU cc_start: 0.6407 (pt0) cc_final: 0.5689 (pm20) REVERT: A 799 MET cc_start: 0.7115 (tpp) cc_final: 0.6879 (tpt) REVERT: A 822 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6423 (mt0) REVERT: B 63 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6323 (pt0) REVERT: B 71 LYS cc_start: 0.5928 (mttt) cc_final: 0.5724 (mttp) REVERT: B 82 MET cc_start: 0.7094 (mtt) cc_final: 0.6724 (mtt) REVERT: B 161 GLU cc_start: 0.6943 (mp0) cc_final: 0.5877 (mp0) REVERT: B 239 ARG cc_start: 0.7113 (ttt-90) cc_final: 0.6893 (ttt180) REVERT: B 313 ASN cc_start: 0.7787 (p0) cc_final: 0.7493 (p0) REVERT: B 360 LYS cc_start: 0.6459 (mttt) cc_final: 0.6052 (mtmm) REVERT: B 573 LYS cc_start: 0.7675 (mttt) cc_final: 0.7007 (mtmm) REVERT: B 587 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7428 (mp) REVERT: B 589 GLU cc_start: 0.6402 (pt0) cc_final: 0.5686 (pm20) REVERT: B 822 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6404 (mt0) outliers start: 19 outliers final: 12 residues processed: 168 average time/residue: 0.3263 time to fit residues: 74.0461 Evaluate side-chains 156 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 0.0770 chunk 68 optimal weight: 0.0170 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 579 HIS B 579 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11708 Z= 0.168 Angle : 0.523 11.425 15878 Z= 0.260 Chirality : 0.038 0.136 1834 Planarity : 0.004 0.042 1994 Dihedral : 3.831 16.694 1574 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.99 % Allowed : 12.58 % Favored : 85.43 % 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: 1.78 (0.22), residues: 1446 helix: 2.33 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -0.91 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 278 HIS 0.006 0.001 HIS B 865 PHE 0.017 0.001 PHE A 473 TYR 0.012 0.001 TYR B 613 ARG 0.003 0.000 ARG A 861 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6375 (pt0) REVERT: A 82 MET cc_start: 0.7117 (mtt) cc_final: 0.6745 (mtt) REVERT: A 119 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4728 (mp0) REVERT: A 120 CYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5418 (m) REVERT: A 161 GLU cc_start: 0.7114 (mp0) cc_final: 0.5957 (mp0) REVERT: A 239 ARG cc_start: 0.7020 (ttt-90) cc_final: 0.6808 (ttt180) REVERT: A 313 ASN cc_start: 0.7865 (p0) cc_final: 0.7613 (p0) REVERT: A 360 LYS cc_start: 0.6550 (mttt) cc_final: 0.6144 (mtmm) REVERT: A 361 TYR cc_start: 0.7791 (t80) cc_final: 0.7487 (t80) REVERT: A 573 LYS cc_start: 0.7759 (mttt) cc_final: 0.7076 (mtmm) REVERT: A 587 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 589 GLU cc_start: 0.6400 (pt0) cc_final: 0.5783 (pm20) REVERT: A 822 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6421 (mt0) REVERT: B 63 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6378 (pt0) REVERT: B 82 MET cc_start: 0.7118 (mtt) cc_final: 0.6750 (mtt) REVERT: B 119 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.4949 (mp0) REVERT: B 161 GLU cc_start: 0.7112 (mp0) cc_final: 0.6665 (mp0) REVERT: B 239 ARG cc_start: 0.7023 (ttt-90) cc_final: 0.6805 (ttt180) REVERT: B 313 ASN cc_start: 0.7857 (p0) cc_final: 0.7613 (p0) REVERT: B 360 LYS cc_start: 0.6537 (mttt) cc_final: 0.6251 (mtmt) REVERT: B 573 LYS cc_start: 0.7718 (mttt) cc_final: 0.7020 (mtmm) REVERT: B 587 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7486 (mp) REVERT: B 589 GLU cc_start: 0.6395 (pt0) cc_final: 0.5771 (pm20) REVERT: B 822 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6414 (mt0) outliers start: 25 outliers final: 14 residues processed: 155 average time/residue: 0.2943 time to fit residues: 62.8689 Evaluate side-chains 144 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 120 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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: 0.7499 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11708 Z= 0.334 Angle : 0.663 13.078 15878 Z= 0.334 Chirality : 0.044 0.166 1834 Planarity : 0.005 0.050 1994 Dihedral : 4.504 20.666 1574 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.63 % Allowed : 12.90 % Favored : 84.47 % 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: 1.20 (0.22), residues: 1446 helix: 1.86 (0.17), residues: 918 sheet: -3.11 (0.89), residues: 24 loop : -1.01 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 278 HIS 0.007 0.001 HIS B 865 PHE 0.021 0.002 PHE B 110 TYR 0.015 0.002 TYR B 613 ARG 0.005 0.001 ARG A 861 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6448 (pt0) REVERT: A 82 MET cc_start: 0.7194 (mtt) cc_final: 0.6835 (mtt) REVERT: A 119 GLU cc_start: 0.5171 (OUTLIER) cc_final: 0.4688 (mp0) REVERT: A 161 GLU cc_start: 0.7317 (mp0) cc_final: 0.7052 (mp0) REVERT: A 239 ARG cc_start: 0.7119 (ttt-90) cc_final: 0.6860 (ttt180) REVERT: A 313 ASN cc_start: 0.7909 (p0) cc_final: 0.7624 (p0) REVERT: A 360 LYS cc_start: 0.6645 (mttt) cc_final: 0.6345 (mtmt) REVERT: A 361 TYR cc_start: 0.7734 (t80) cc_final: 0.7510 (t80) REVERT: A 573 LYS cc_start: 0.7981 (mttt) cc_final: 0.7271 (mtmm) REVERT: A 587 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7435 (mp) REVERT: A 589 GLU cc_start: 0.6390 (pt0) cc_final: 0.5833 (pm20) REVERT: A 822 GLN cc_start: 0.7045 (mm-40) cc_final: 0.6381 (mt0) REVERT: B 63 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6450 (pt0) REVERT: B 82 MET cc_start: 0.7196 (mtt) cc_final: 0.6841 (mtt) REVERT: B 116 SER cc_start: 0.7176 (m) cc_final: 0.6723 (t) REVERT: B 119 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.5010 (mp0) REVERT: B 120 CYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5273 (m) REVERT: B 161 GLU cc_start: 0.7335 (mp0) cc_final: 0.7065 (mp0) REVERT: B 239 ARG cc_start: 0.7122 (ttt-90) cc_final: 0.6862 (ttt180) REVERT: B 313 ASN cc_start: 0.7900 (p0) cc_final: 0.7627 (p0) REVERT: B 360 LYS cc_start: 0.6606 (mttt) cc_final: 0.6305 (mtmt) REVERT: B 573 LYS cc_start: 0.7981 (mttt) cc_final: 0.7273 (mtmm) REVERT: B 587 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7435 (mp) REVERT: B 589 GLU cc_start: 0.6382 (pt0) cc_final: 0.5828 (pm20) REVERT: B 822 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6364 (mt0) outliers start: 33 outliers final: 20 residues processed: 162 average time/residue: 0.2818 time to fit residues: 63.3807 Evaluate side-chains 151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.0970 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7476 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11708 Z= 0.244 Angle : 0.570 11.858 15878 Z= 0.287 Chirality : 0.040 0.229 1834 Planarity : 0.005 0.044 1994 Dihedral : 4.215 21.108 1574 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.55 % Allowed : 13.46 % Favored : 84.00 % 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: 1.26 (0.22), residues: 1446 helix: 2.02 (0.17), residues: 908 sheet: -3.23 (0.88), residues: 24 loop : -1.18 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.007 0.001 HIS A 865 PHE 0.021 0.001 PHE A 429 TYR 0.011 0.001 TYR B 613 ARG 0.003 0.000 ARG A 861 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6406 (pt0) REVERT: A 82 MET cc_start: 0.7185 (mtt) cc_final: 0.6852 (mtt) REVERT: A 119 GLU cc_start: 0.4936 (OUTLIER) cc_final: 0.4640 (mp0) REVERT: A 161 GLU cc_start: 0.7370 (mp0) cc_final: 0.6901 (mp0) REVERT: A 239 ARG cc_start: 0.7063 (ttt-90) cc_final: 0.6820 (ttt180) REVERT: A 313 ASN cc_start: 0.7898 (p0) cc_final: 0.7657 (p0) REVERT: A 360 LYS cc_start: 0.6620 (mttt) cc_final: 0.6215 (mtmm) REVERT: A 361 TYR cc_start: 0.7769 (t80) cc_final: 0.7518 (t80) REVERT: A 444 ASN cc_start: 0.7614 (m-40) cc_final: 0.7378 (m-40) REVERT: A 573 LYS cc_start: 0.8025 (mttt) cc_final: 0.6702 (mmtm) REVERT: A 587 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7438 (mp) REVERT: A 589 GLU cc_start: 0.6400 (pt0) cc_final: 0.5843 (pm20) REVERT: A 670 GLU cc_start: 0.7446 (tp30) cc_final: 0.7033 (tp30) REVERT: A 822 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6413 (mt0) REVERT: B 63 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6407 (pt0) REVERT: B 82 MET cc_start: 0.7185 (mtt) cc_final: 0.6857 (mtt) REVERT: B 116 SER cc_start: 0.7228 (m) cc_final: 0.6874 (t) REVERT: B 120 CYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5238 (m) REVERT: B 161 GLU cc_start: 0.7370 (mp0) cc_final: 0.6902 (mp0) REVERT: B 239 ARG cc_start: 0.7016 (ttt-90) cc_final: 0.6767 (ttt180) REVERT: B 313 ASN cc_start: 0.7866 (p0) cc_final: 0.7629 (p0) REVERT: B 360 LYS cc_start: 0.6644 (mttt) cc_final: 0.6228 (mtmm) REVERT: B 436 ASN cc_start: 0.6684 (t0) cc_final: 0.6464 (t0) REVERT: B 508 LYS cc_start: 0.6838 (mmtp) cc_final: 0.6616 (mptt) REVERT: B 573 LYS cc_start: 0.8026 (mttt) cc_final: 0.6705 (mmtm) REVERT: B 587 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7440 (mp) REVERT: B 589 GLU cc_start: 0.6400 (pt0) cc_final: 0.5843 (pm20) REVERT: B 670 GLU cc_start: 0.7437 (tp30) cc_final: 0.7026 (tp30) REVERT: B 822 GLN cc_start: 0.6979 (mm-40) cc_final: 0.6405 (mt0) outliers start: 32 outliers final: 26 residues processed: 142 average time/residue: 0.3307 time to fit residues: 64.7539 Evaluate side-chains 148 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11708 Z= 0.186 Angle : 0.522 11.247 15878 Z= 0.263 Chirality : 0.038 0.141 1834 Planarity : 0.004 0.044 1994 Dihedral : 4.030 20.700 1574 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.23 % Allowed : 13.85 % Favored : 83.92 % 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 (0.22), residues: 1446 helix: 2.20 (0.17), residues: 912 sheet: -3.33 (0.88), residues: 24 loop : -1.12 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.009 0.001 HIS A 865 PHE 0.016 0.001 PHE B 110 TYR 0.009 0.001 TYR B 613 ARG 0.005 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6303 (pt0) REVERT: A 82 MET cc_start: 0.7200 (mtt) cc_final: 0.6878 (mtt) REVERT: A 161 GLU cc_start: 0.7310 (mp0) cc_final: 0.6854 (mt-10) REVERT: A 239 ARG cc_start: 0.6925 (ttt-90) cc_final: 0.6695 (ttt180) REVERT: A 313 ASN cc_start: 0.7891 (p0) cc_final: 0.7685 (p0) REVERT: A 360 LYS cc_start: 0.6608 (mttt) cc_final: 0.6306 (mtmt) REVERT: A 361 TYR cc_start: 0.7779 (t80) cc_final: 0.7525 (t80) REVERT: A 444 ASN cc_start: 0.7502 (m-40) cc_final: 0.7255 (m-40) REVERT: A 573 LYS cc_start: 0.7985 (mttt) cc_final: 0.6696 (mmtm) REVERT: A 587 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7471 (mp) REVERT: A 589 GLU cc_start: 0.6422 (pt0) cc_final: 0.5847 (pm20) REVERT: A 670 GLU cc_start: 0.7460 (tp30) cc_final: 0.7054 (tp30) REVERT: A 822 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6401 (mt0) REVERT: B 63 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6308 (pt0) REVERT: B 82 MET cc_start: 0.7199 (mtt) cc_final: 0.6881 (mtt) REVERT: B 120 CYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5653 (m) REVERT: B 125 CYS cc_start: 0.4917 (OUTLIER) cc_final: 0.4270 (p) REVERT: B 161 GLU cc_start: 0.7309 (mp0) cc_final: 0.6852 (mt-10) REVERT: B 239 ARG cc_start: 0.6928 (ttt-90) cc_final: 0.6699 (ttt180) REVERT: B 313 ASN cc_start: 0.7834 (p0) cc_final: 0.7624 (p0) REVERT: B 360 LYS cc_start: 0.6632 (mttt) cc_final: 0.6312 (mtmt) REVERT: B 508 LYS cc_start: 0.6866 (mmtp) cc_final: 0.6574 (mttt) REVERT: B 573 LYS cc_start: 0.7982 (mttt) cc_final: 0.6691 (mmtm) REVERT: B 587 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7469 (mp) REVERT: B 589 GLU cc_start: 0.6419 (pt0) cc_final: 0.5846 (pm20) REVERT: B 670 GLU cc_start: 0.7451 (tp30) cc_final: 0.7047 (tp30) REVERT: B 822 GLN cc_start: 0.6985 (mm-40) cc_final: 0.6401 (mt0) outliers start: 28 outliers final: 18 residues processed: 140 average time/residue: 0.3209 time to fit residues: 62.1486 Evaluate side-chains 139 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 0.0070 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7418 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11708 Z= 0.142 Angle : 0.492 9.716 15878 Z= 0.247 Chirality : 0.037 0.137 1834 Planarity : 0.004 0.044 1994 Dihedral : 3.796 18.527 1574 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 1.59 % Allowed : 14.73 % Favored : 83.68 % 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: 1.66 (0.22), residues: 1446 helix: 2.34 (0.17), residues: 918 sheet: -3.49 (0.88), residues: 24 loop : -1.08 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 590 HIS 0.008 0.001 HIS A 865 PHE 0.014 0.001 PHE A 473 TYR 0.008 0.001 TYR B 613 ARG 0.002 0.000 ARG B 861 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.400 Fit side-chains REVERT: A 63 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6317 (pt0) REVERT: A 82 MET cc_start: 0.7207 (mtt) cc_final: 0.6908 (mtt) REVERT: A 161 GLU cc_start: 0.7299 (mp0) cc_final: 0.6794 (mt-10) REVERT: A 239 ARG cc_start: 0.6914 (ttt-90) cc_final: 0.6699 (ttt180) REVERT: A 360 LYS cc_start: 0.6573 (mttt) cc_final: 0.6242 (mtmt) REVERT: A 361 TYR cc_start: 0.7804 (t80) cc_final: 0.7530 (t80) REVERT: A 508 LYS cc_start: 0.6422 (mptt) cc_final: 0.6182 (mptt) REVERT: A 573 LYS cc_start: 0.7892 (mttt) cc_final: 0.7161 (mtmm) REVERT: A 587 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 670 GLU cc_start: 0.7420 (tp30) cc_final: 0.7025 (tp30) REVERT: A 764 GLN cc_start: 0.7799 (tp40) cc_final: 0.7048 (tt0) REVERT: A 822 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6397 (mt0) REVERT: B 63 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6325 (pt0) REVERT: B 82 MET cc_start: 0.7210 (mtt) cc_final: 0.6914 (mtt) REVERT: B 120 CYS cc_start: 0.6343 (OUTLIER) cc_final: 0.5140 (m) REVERT: B 161 GLU cc_start: 0.7295 (mp0) cc_final: 0.6792 (mt-10) REVERT: B 239 ARG cc_start: 0.6918 (ttt-90) cc_final: 0.6703 (ttt180) REVERT: B 360 LYS cc_start: 0.6567 (mttt) cc_final: 0.6245 (mtmt) REVERT: B 508 LYS cc_start: 0.6853 (mmtp) cc_final: 0.6558 (mttt) REVERT: B 573 LYS cc_start: 0.7889 (mttt) cc_final: 0.7162 (mtmm) REVERT: B 587 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7542 (mp) REVERT: B 670 GLU cc_start: 0.7411 (tp30) cc_final: 0.7020 (tp30) REVERT: B 764 GLN cc_start: 0.7869 (tp40) cc_final: 0.7132 (tt0) REVERT: B 822 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6402 (mt0) outliers start: 20 outliers final: 17 residues processed: 137 average time/residue: 0.3066 time to fit residues: 58.1565 Evaluate side-chains 139 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11708 Z= 0.308 Angle : 0.598 11.398 15878 Z= 0.301 Chirality : 0.042 0.155 1834 Planarity : 0.005 0.044 1994 Dihedral : 4.200 19.181 1574 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.63 % Allowed : 14.01 % Favored : 83.36 % 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: 1.34 (0.22), residues: 1446 helix: 2.08 (0.17), residues: 918 sheet: -3.34 (0.89), residues: 24 loop : -1.19 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 278 HIS 0.007 0.001 HIS B 865 PHE 0.019 0.002 PHE A 110 TYR 0.013 0.001 TYR B 613 ARG 0.005 0.000 ARG A 861 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6440 (pt0) REVERT: A 82 MET cc_start: 0.7218 (mtt) cc_final: 0.6901 (mtt) REVERT: A 161 GLU cc_start: 0.7390 (mp0) cc_final: 0.6916 (mt-10) REVERT: A 239 ARG cc_start: 0.7080 (ttt-90) cc_final: 0.6822 (ttt180) REVERT: A 360 LYS cc_start: 0.6601 (mttt) cc_final: 0.6313 (mtmt) REVERT: A 444 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: A 508 LYS cc_start: 0.6482 (mptt) cc_final: 0.6129 (mttt) REVERT: A 573 LYS cc_start: 0.8083 (mttt) cc_final: 0.6767 (mmtm) REVERT: A 587 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7442 (mp) REVERT: A 670 GLU cc_start: 0.7497 (tp30) cc_final: 0.7104 (tp30) REVERT: A 822 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6401 (mt0) REVERT: B 63 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6441 (pt0) REVERT: B 82 MET cc_start: 0.7217 (mtt) cc_final: 0.6902 (mtt) REVERT: B 120 CYS cc_start: 0.6488 (OUTLIER) cc_final: 0.5479 (m) REVERT: B 161 GLU cc_start: 0.7389 (mp0) cc_final: 0.6917 (mt-10) REVERT: B 239 ARG cc_start: 0.7080 (ttt-90) cc_final: 0.6822 (ttt180) REVERT: B 360 LYS cc_start: 0.6635 (mttt) cc_final: 0.6321 (mtmt) REVERT: B 508 LYS cc_start: 0.7052 (mmtp) cc_final: 0.6815 (mttt) REVERT: B 573 LYS cc_start: 0.8083 (mttt) cc_final: 0.6767 (mmtm) REVERT: B 587 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7444 (mp) REVERT: B 670 GLU cc_start: 0.7495 (tp30) cc_final: 0.7101 (tp30) REVERT: B 822 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6402 (mt0) outliers start: 33 outliers final: 24 residues processed: 140 average time/residue: 0.3060 time to fit residues: 58.4232 Evaluate side-chains 145 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.0060 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 GLN B 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11708 Z= 0.162 Angle : 0.527 10.603 15878 Z= 0.264 Chirality : 0.038 0.136 1834 Planarity : 0.004 0.043 1994 Dihedral : 3.950 19.507 1574 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.75 % Allowed : 14.89 % Favored : 83.36 % 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 (0.22), residues: 1446 helix: 2.30 (0.17), residues: 916 sheet: -3.46 (0.88), residues: 24 loop : -1.15 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.008 0.001 HIS A 865 PHE 0.015 0.001 PHE B 110 TYR 0.009 0.001 TYR B 613 ARG 0.004 0.000 ARG B 861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.480 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6353 (pt0) REVERT: A 82 MET cc_start: 0.7257 (mtt) cc_final: 0.6951 (mtt) REVERT: A 132 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: A 161 GLU cc_start: 0.7382 (mp0) cc_final: 0.6921 (mt-10) REVERT: A 239 ARG cc_start: 0.6916 (ttt-90) cc_final: 0.6696 (ttt180) REVERT: A 360 LYS cc_start: 0.6628 (mttt) cc_final: 0.6304 (mtmt) REVERT: A 508 LYS cc_start: 0.6383 (mptt) cc_final: 0.6024 (mttt) REVERT: A 573 LYS cc_start: 0.7989 (mttt) cc_final: 0.6684 (mmtm) REVERT: A 587 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7572 (mp) REVERT: A 670 GLU cc_start: 0.7445 (tp30) cc_final: 0.7055 (tp30) REVERT: A 764 GLN cc_start: 0.7823 (tp40) cc_final: 0.7083 (tt0) REVERT: A 822 GLN cc_start: 0.6980 (mm-40) cc_final: 0.6390 (mt0) REVERT: B 63 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6354 (pt0) REVERT: B 82 MET cc_start: 0.7253 (mtt) cc_final: 0.6955 (mtt) REVERT: B 120 CYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5618 (m) REVERT: B 161 GLU cc_start: 0.7378 (mp0) cc_final: 0.6920 (mt-10) REVERT: B 239 ARG cc_start: 0.6917 (ttt-90) cc_final: 0.6697 (ttt180) REVERT: B 360 LYS cc_start: 0.6547 (mttt) cc_final: 0.6211 (mtmt) REVERT: B 444 ASN cc_start: 0.7308 (m-40) cc_final: 0.7085 (m-40) REVERT: B 508 LYS cc_start: 0.6868 (mmtp) cc_final: 0.6626 (mttm) REVERT: B 573 LYS cc_start: 0.7989 (mttt) cc_final: 0.6683 (mmtm) REVERT: B 587 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7572 (mp) REVERT: B 670 GLU cc_start: 0.7450 (tp30) cc_final: 0.7067 (tp30) REVERT: B 822 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6393 (mt0) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.3167 time to fit residues: 56.9218 Evaluate side-chains 137 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 0.0770 chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 119 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.134688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.120670 restraints weight = 12496.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.104507 restraints weight = 26670.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.104097 restraints weight = 22602.329| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11708 Z= 0.191 Angle : 0.539 11.042 15878 Z= 0.269 Chirality : 0.038 0.140 1834 Planarity : 0.004 0.043 1994 Dihedral : 3.932 17.615 1574 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.23 % Allowed : 14.81 % Favored : 82.96 % 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: 1.58 (0.22), residues: 1446 helix: 2.30 (0.17), residues: 916 sheet: -3.45 (0.89), residues: 24 loop : -1.14 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 278 HIS 0.007 0.001 HIS B 865 PHE 0.015 0.001 PHE B 110 TYR 0.009 0.001 TYR B 613 ARG 0.004 0.000 ARG A 861 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.94 seconds wall clock time: 46 minutes 50.67 seconds (2810.67 seconds total)