Starting phenix.real_space_refine on Mon Dec 30 09:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a9a_15274/12_2024/8a9a_15274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a9a_15274/12_2024/8a9a_15274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a9a_15274/12_2024/8a9a_15274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a9a_15274/12_2024/8a9a_15274.map" model { file = "/net/cci-nas-00/data/ceres_data/8a9a_15274/12_2024/8a9a_15274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a9a_15274/12_2024/8a9a_15274.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 16 5.16 5 C 8240 2.51 5 N 2054 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12772 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6386 Classifications: {'peptide': 809} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 786} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: B Time building chain proxies: 14.42, per 1000 atoms: 1.13 Number of scatterers: 12772 At special positions: 0 Unit cell: (86.1, 115.5, 257.25, 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 16 16.00 O 2462 8.00 N 2054 7.00 C 8240 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 - 3.00 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 6 sheets defined 46.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'B' and resid 95 through 106 removed outlier: 4.063A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 125 removed outlier: 3.766A pdb=" N ALA B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.171A pdb=" N ASN B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 Processing helix chain 'B' and resid 268 through 294 removed outlier: 3.554A pdb=" N ILE B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.649A pdb=" N GLU B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 removed outlier: 4.023A pdb=" N LYS B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 removed outlier: 3.708A pdb=" N ARG B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 removed outlier: 3.663A pdb=" N LYS B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.598A pdb=" N ASP B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.866A pdb=" N SER B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 393 through 415 removed outlier: 4.583A pdb=" N ASP B 406 " --> pdb=" O GLN B 402 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Proline residue: B 410 - end of helix Processing helix chain 'B' and resid 421 through 429 removed outlier: 3.690A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 443 through 462 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.882A pdb=" N LEU B 484 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 486 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 499 removed outlier: 4.189A pdb=" N ALA B 495 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.976A pdb=" N ASP B 514 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.108A pdb=" N GLU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 557' Processing helix chain 'B' and resid 565 through 584 removed outlier: 4.136A pdb=" N GLU B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 removed outlier: 4.018A pdb=" N LYS B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.584A pdb=" N LEU B 644 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 Processing helix chain 'B' and resid 663 through 674 Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.819A pdb=" N PHE B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'B' and resid 719 through 723 Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'A' and resid 95 through 106 removed outlier: 4.062A pdb=" N GLY A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 125 removed outlier: 3.767A pdb=" N ALA A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.171A pdb=" N ASN A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.554A pdb=" N ILE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.649A pdb=" N GLU A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 removed outlier: 4.023A pdb=" N LYS A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.708A pdb=" N ARG A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.663A pdb=" N LYS A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.598A pdb=" N ASP A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.867A pdb=" N SER A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 393 through 415 removed outlier: 4.584A pdb=" N ASP A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Proline residue: A 410 - end of helix Processing helix chain 'A' and resid 421 through 429 removed outlier: 3.690A pdb=" N ILE A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 486 removed outlier: 3.882A pdb=" N LEU A 484 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 removed outlier: 4.189A pdb=" N ALA A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.977A pdb=" N ASP A 514 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 532 through 540 Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.110A pdb=" N GLU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'A' and resid 565 through 584 removed outlier: 4.137A pdb=" N GLU A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.017A pdb=" N LYS A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.583A pdb=" N LEU A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.818A pdb=" N PHE A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 797 through 816 Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 143 removed outlier: 5.485A pdb=" N LEU B 136 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR B 160 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG B 158 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 140 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 151 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA B 193 " --> pdb=" O ALA B 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 184 through 194 current: chain 'B' and resid 211 through 219 removed outlier: 7.590A pdb=" N MET B 213 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER B 228 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 215 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 217 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.551A pdb=" N VAL B 179 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 595 through 598 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 595 through 598 current: chain 'B' and resid 615 through 620 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 615 through 620 current: chain 'B' and resid 728 through 750 removed outlier: 9.593A pdb=" N TYR B 740 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N ILE B 770 " --> pdb=" O TYR B 740 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N GLY B 742 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N THR B 768 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASN B 744 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N VAL B 766 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 746 " --> pdb=" O ILE B 764 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 143 removed outlier: 5.485A pdb=" N LEU A 136 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 160 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG A 158 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 140 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 151 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA A 193 " --> pdb=" O ALA A 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 194 current: chain 'A' and resid 211 through 219 removed outlier: 7.589A pdb=" N MET A 213 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N SER A 228 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP A 215 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 217 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.552A pdb=" N VAL A 179 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 598 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 595 through 598 current: chain 'A' and resid 615 through 620 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 615 through 620 current: chain 'A' and resid 728 through 750 removed outlier: 9.594A pdb=" N TYR A 740 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N ILE A 770 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLY A 742 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N THR A 768 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASN A 744 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N VAL A 766 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 746 " --> pdb=" O ILE A 764 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1332 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: 3.68 Time building geometry restraints manager: 3.66 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: 4078 1.34 - 1.46: 2682 1.46 - 1.58: 6202 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 12994 Sorted by residual: bond pdb=" CB LYS A 363 " pdb=" CG LYS A 363 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB LYS B 363 " pdb=" CG LYS B 363 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" N PRO B 61 " pdb=" CA PRO B 61 " ideal model delta sigma weight residual 1.469 1.454 0.014 1.28e-02 6.10e+03 1.26e+00 bond pdb=" N PRO A 61 " pdb=" CA PRO A 61 " ideal model delta sigma weight residual 1.469 1.455 0.014 1.28e-02 6.10e+03 1.23e+00 bond pdb=" CB ASN B 328 " pdb=" CG ASN B 328 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.11e-01 ... (remaining 12989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 17081 1.80 - 3.60: 340 3.60 - 5.40: 53 5.40 - 7.20: 22 7.20 - 9.00: 16 Bond angle restraints: 17512 Sorted by residual: angle pdb=" N PRO A 61 " pdb=" CA PRO A 61 " pdb=" CB PRO A 61 " ideal model delta sigma weight residual 103.25 110.58 -7.33 1.05e+00 9.07e-01 4.88e+01 angle pdb=" N PRO B 61 " pdb=" CA PRO B 61 " pdb=" CB PRO B 61 " ideal model delta sigma weight residual 103.25 110.55 -7.30 1.05e+00 9.07e-01 4.83e+01 angle pdb=" N LEU B 546 " pdb=" CA LEU B 546 " pdb=" C LEU B 546 " ideal model delta sigma weight residual 114.31 109.99 4.32 1.29e+00 6.01e-01 1.12e+01 angle pdb=" N LEU A 546 " pdb=" CA LEU A 546 " pdb=" C LEU A 546 " ideal model delta sigma weight residual 114.31 110.03 4.28 1.29e+00 6.01e-01 1.10e+01 angle pdb=" CA LYS B 363 " pdb=" CB LYS B 363 " pdb=" CG LYS B 363 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 17507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6597 17.65 - 35.29: 991 35.29 - 52.94: 244 52.94 - 70.59: 46 70.59 - 88.24: 20 Dihedral angle restraints: 7898 sinusoidal: 3178 harmonic: 4720 Sorted by residual: dihedral pdb=" CA PHE B 817 " pdb=" C PHE B 817 " pdb=" N GLN B 818 " pdb=" CA GLN B 818 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE A 817 " pdb=" C PHE A 817 " pdb=" N GLN A 818 " pdb=" CA GLN A 818 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU B 524 " pdb=" C LEU B 524 " pdb=" N LEU B 525 " pdb=" CA LEU B 525 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1509 0.044 - 0.088: 378 0.088 - 0.132: 94 0.132 - 0.176: 11 0.176 - 0.219: 6 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CA PRO B 61 " pdb=" N PRO B 61 " pdb=" C PRO B 61 " pdb=" CB PRO B 61 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO A 61 " pdb=" N PRO A 61 " pdb=" C PRO A 61 " pdb=" CB PRO A 61 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PHE B 111 " pdb=" N PHE B 111 " pdb=" C PHE B 111 " pdb=" CB PHE B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1995 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 331 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO B 332 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 332 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 332 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 331 " 0.059 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A 332 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 375 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.045 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 265 2.67 - 3.23: 12490 3.23 - 3.79: 19940 3.79 - 4.34: 27205 4.34 - 4.90: 44018 Nonbonded interactions: 103918 Sorted by model distance: nonbonded pdb=" OG1 THR B 144 " pdb=" OG SER B 152 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR A 144 " pdb=" OG SER A 152 " model vdw 2.117 3.040 nonbonded pdb=" O THR A 610 " pdb=" OG1 THR A 613 " model vdw 2.201 3.040 nonbonded pdb=" O THR B 610 " pdb=" OG1 THR B 613 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 816 " pdb=" OH TYR B 821 " model vdw 2.233 3.040 ... (remaining 103913 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.870 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.130 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 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 0.036 12994 Z= 0.190 Angle : 0.666 8.999 17512 Z= 0.345 Chirality : 0.043 0.219 1998 Planarity : 0.005 0.090 2242 Dihedral : 18.003 88.236 4838 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.53 % Favored : 89.10 % Rotamer: Outliers : 0.14 % Allowed : 29.36 % Favored : 70.50 % 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: -1.45 (0.21), residues: 1614 helix: 0.19 (0.21), residues: 640 sheet: -0.07 (0.46), residues: 136 loop : -2.12 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 681 HIS 0.005 0.001 HIS B 580 PHE 0.016 0.001 PHE B 485 TYR 0.010 0.001 TYR A 761 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 LEU cc_start: 0.8492 (mt) cc_final: 0.8268 (mt) REVERT: B 465 MET cc_start: 0.5288 (mmp) cc_final: 0.5043 (mmm) REVERT: B 711 PHE cc_start: 0.7701 (m-80) cc_final: 0.7487 (m-80) REVERT: A 534 ASP cc_start: 0.4215 (t70) cc_final: 0.3934 (t0) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.2834 time to fit residues: 113.6934 Evaluate side-chains 148 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 781 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 93 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN B 279 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 746 ASN A 235 ASN A 584 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN A 803 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12994 Z= 0.393 Angle : 0.792 8.483 17512 Z= 0.409 Chirality : 0.049 0.259 1998 Planarity : 0.005 0.073 2242 Dihedral : 5.499 34.226 1682 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.21 % Favored : 88.48 % Rotamer: Outliers : 5.43 % Allowed : 24.36 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1614 helix: -0.56 (0.20), residues: 648 sheet: -0.69 (0.44), residues: 156 loop : -1.99 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 681 HIS 0.008 0.002 HIS B 580 PHE 0.021 0.002 PHE B 458 TYR 0.023 0.002 TYR A 623 ARG 0.005 0.001 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 148 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.6469 (ppp) cc_final: 0.6073 (ppp) REVERT: B 695 ASN cc_start: 0.7545 (t0) cc_final: 0.7178 (t0) REVERT: A 393 ASP cc_start: 0.4235 (OUTLIER) cc_final: 0.3709 (t70) REVERT: A 500 THR cc_start: 0.7551 (m) cc_final: 0.6810 (p) outliers start: 76 outliers final: 31 residues processed: 217 average time/residue: 0.2484 time to fit residues: 80.2186 Evaluate side-chains 151 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 773 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 129 optimal weight: 0.0060 chunk 144 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 116 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 746 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 449 ASN ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12994 Z= 0.231 Angle : 0.662 12.356 17512 Z= 0.339 Chirality : 0.044 0.156 1998 Planarity : 0.004 0.054 2242 Dihedral : 5.126 26.799 1680 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.98 % Favored : 89.71 % Rotamer: Outliers : 4.79 % Allowed : 25.57 % Favored : 69.64 % 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: -1.95 (0.20), residues: 1614 helix: -0.52 (0.19), residues: 656 sheet: -0.61 (0.45), residues: 144 loop : -2.12 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.005 0.001 HIS A 580 PHE 0.018 0.001 PHE B 232 TYR 0.018 0.001 TYR B 79 ARG 0.006 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 136 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7768 (tt) REVERT: B 695 ASN cc_start: 0.7349 (t0) cc_final: 0.7056 (t0) REVERT: B 864 LEU cc_start: 0.4781 (tp) cc_final: 0.4530 (tp) REVERT: A 347 GLN cc_start: 0.6352 (tp-100) cc_final: 0.5475 (mp10) REVERT: A 427 GLU cc_start: 0.2598 (OUTLIER) cc_final: 0.0895 (mt-10) REVERT: A 496 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7701 (tt0) REVERT: A 500 THR cc_start: 0.7525 (m) cc_final: 0.6780 (p) REVERT: A 668 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7165 (tttt) outliers start: 67 outliers final: 33 residues processed: 194 average time/residue: 0.2238 time to fit residues: 67.2738 Evaluate side-chains 152 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9980 chunk 109 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 367 ASN A 304 GLN ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12994 Z= 0.206 Angle : 0.644 13.255 17512 Z= 0.329 Chirality : 0.043 0.159 1998 Planarity : 0.004 0.046 2242 Dihedral : 4.991 21.959 1680 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.10 % Favored : 89.65 % Rotamer: Outliers : 5.36 % Allowed : 25.07 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1614 helix: -0.54 (0.19), residues: 660 sheet: -1.21 (0.40), residues: 178 loop : -2.05 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 121 HIS 0.006 0.001 HIS A 580 PHE 0.023 0.001 PHE B 454 TYR 0.014 0.001 TYR B 79 ARG 0.006 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 122 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.6304 (ppp) cc_final: 0.6050 (ppp) REVERT: B 341 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7754 (tt) REVERT: B 637 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6969 (tt) REVERT: B 667 MET cc_start: 0.7055 (tmm) cc_final: 0.6767 (tmm) REVERT: B 695 ASN cc_start: 0.7225 (t0) cc_final: 0.6924 (t0) REVERT: B 864 LEU cc_start: 0.4664 (tp) cc_final: 0.4438 (tp) REVERT: A 97 LEU cc_start: 0.2013 (OUTLIER) cc_final: 0.1706 (pt) REVERT: A 347 GLN cc_start: 0.6415 (tp-100) cc_final: 0.5495 (mp10) REVERT: A 427 GLU cc_start: 0.3368 (OUTLIER) cc_final: 0.1393 (mp0) REVERT: A 496 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8062 (tt0) REVERT: A 668 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7103 (tttt) outliers start: 75 outliers final: 41 residues processed: 189 average time/residue: 0.2420 time to fit residues: 71.8955 Evaluate side-chains 151 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 115 optimal weight: 0.0010 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 718 ASN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12994 Z= 0.251 Angle : 0.672 9.948 17512 Z= 0.341 Chirality : 0.044 0.161 1998 Planarity : 0.004 0.042 2242 Dihedral : 5.138 23.969 1680 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.72 % Favored : 89.10 % Rotamer: Outliers : 5.21 % Allowed : 25.29 % Favored : 69.50 % 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: -2.05 (0.20), residues: 1614 helix: -0.64 (0.19), residues: 652 sheet: -0.96 (0.44), residues: 154 loop : -2.07 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 121 HIS 0.006 0.001 HIS A 580 PHE 0.017 0.002 PHE B 232 TYR 0.011 0.001 TYR A 623 ARG 0.009 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.6508 (ppp) cc_final: 0.6170 (ppp) REVERT: B 341 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 427 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.4970 (pt0) REVERT: B 637 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7091 (tt) REVERT: B 695 ASN cc_start: 0.7289 (t0) cc_final: 0.7042 (t0) REVERT: B 864 LEU cc_start: 0.4677 (tp) cc_final: 0.4438 (tp) REVERT: A 294 MET cc_start: 0.7481 (ptm) cc_final: 0.7152 (ptt) REVERT: A 347 GLN cc_start: 0.6397 (tp-100) cc_final: 0.5330 (mp10) REVERT: A 364 THR cc_start: 0.5053 (OUTLIER) cc_final: 0.4597 (m) REVERT: A 496 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8172 (tt0) REVERT: A 668 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7125 (tttt) REVERT: A 799 GLN cc_start: 0.7241 (tm130) cc_final: 0.6960 (tm-30) outliers start: 73 outliers final: 43 residues processed: 191 average time/residue: 0.2284 time to fit residues: 66.4409 Evaluate side-chains 157 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 30 optimal weight: 0.0030 chunk 90 optimal weight: 30.0000 chunk 38 optimal weight: 0.0970 chunk 154 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 0.3980 chunk 81 optimal weight: 30.0000 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN A 277 ASN A 303 ASN A 343 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12994 Z= 0.202 Angle : 0.654 9.835 17512 Z= 0.330 Chirality : 0.043 0.147 1998 Planarity : 0.004 0.040 2242 Dihedral : 5.023 23.490 1680 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.98 % Favored : 89.78 % Rotamer: Outliers : 4.86 % Allowed : 26.29 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1614 helix: -0.58 (0.19), residues: 658 sheet: -1.04 (0.43), residues: 158 loop : -2.11 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 121 HIS 0.006 0.001 HIS A 580 PHE 0.028 0.001 PHE B 454 TYR 0.014 0.001 TYR B 79 ARG 0.009 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 120 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 404 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: B 427 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.4925 (pt0) REVERT: B 637 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6996 (tt) REVERT: B 695 ASN cc_start: 0.7208 (t0) cc_final: 0.7002 (t0) REVERT: B 864 LEU cc_start: 0.4659 (tp) cc_final: 0.4406 (tp) REVERT: A 364 THR cc_start: 0.4753 (OUTLIER) cc_final: 0.4282 (m) REVERT: A 668 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7215 (tttt) outliers start: 68 outliers final: 48 residues processed: 180 average time/residue: 0.2382 time to fit residues: 66.0650 Evaluate side-chains 156 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.0000 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN A 216 HIS A 343 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 12994 Z= 0.528 Angle : 0.898 11.667 17512 Z= 0.460 Chirality : 0.051 0.231 1998 Planarity : 0.005 0.052 2242 Dihedral : 6.043 25.382 1680 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.70 % Favored : 86.99 % Rotamer: Outliers : 5.36 % Allowed : 26.14 % Favored : 68.50 % 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: -2.62 (0.19), residues: 1614 helix: -1.20 (0.19), residues: 654 sheet: -0.96 (0.47), residues: 128 loop : -2.34 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 121 HIS 0.009 0.002 HIS A 580 PHE 0.026 0.003 PHE A 327 TYR 0.021 0.002 TYR A 752 ARG 0.007 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 119 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8322 (tt) REVERT: B 341 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7788 (tt) REVERT: B 404 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: B 474 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7024 (mt-10) REVERT: B 695 ASN cc_start: 0.7590 (t0) cc_final: 0.7207 (t0) REVERT: A 294 MET cc_start: 0.7710 (ptm) cc_final: 0.7457 (ptt) REVERT: A 364 THR cc_start: 0.5476 (OUTLIER) cc_final: 0.4774 (m) REVERT: A 502 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.6990 (mtm180) REVERT: A 668 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7020 (tttt) outliers start: 75 outliers final: 43 residues processed: 185 average time/residue: 0.2206 time to fit residues: 62.8858 Evaluate side-chains 153 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 76 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12994 Z= 0.209 Angle : 0.693 9.441 17512 Z= 0.354 Chirality : 0.044 0.164 1998 Planarity : 0.004 0.049 2242 Dihedral : 5.457 26.623 1680 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.54 % Favored : 90.21 % Rotamer: Outliers : 4.07 % Allowed : 27.93 % Favored : 68.00 % 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: -2.34 (0.20), residues: 1614 helix: -0.96 (0.19), residues: 674 sheet: -0.73 (0.49), residues: 128 loop : -2.24 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 121 HIS 0.004 0.001 HIS B 580 PHE 0.050 0.001 PHE B 159 TYR 0.025 0.001 TYR A 740 ARG 0.009 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7766 (tt) REVERT: B 404 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: B 427 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5415 (pt0) REVERT: B 431 GLN cc_start: 0.6796 (pm20) cc_final: 0.6543 (pm20) REVERT: B 474 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6198 (pt0) REVERT: B 620 ASP cc_start: 0.6289 (p0) cc_final: 0.5880 (p0) REVERT: B 695 ASN cc_start: 0.7255 (t0) cc_final: 0.6960 (t0) REVERT: A 294 MET cc_start: 0.7621 (ptm) cc_final: 0.7367 (ptt) REVERT: A 364 THR cc_start: 0.4616 (OUTLIER) cc_final: 0.4118 (m) REVERT: A 450 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6137 (pp) REVERT: A 499 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8038 (mt) REVERT: A 597 LYS cc_start: 0.4644 (pttm) cc_final: 0.4440 (mttp) REVERT: A 668 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7265 (tttt) outliers start: 57 outliers final: 42 residues processed: 173 average time/residue: 0.2325 time to fit residues: 61.9155 Evaluate side-chains 156 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 134 optimal weight: 0.0970 chunk 143 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 129 optimal weight: 0.0770 chunk 135 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 361 ASN B 453 ASN A 277 ASN A 303 ASN A 343 GLN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12994 Z= 0.186 Angle : 0.681 12.499 17512 Z= 0.345 Chirality : 0.043 0.156 1998 Planarity : 0.004 0.043 2242 Dihedral : 5.209 24.678 1680 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.66 % Favored : 89.10 % Rotamer: Outliers : 4.21 % Allowed : 27.86 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.20), residues: 1614 helix: -0.74 (0.19), residues: 674 sheet: -0.58 (0.50), residues: 128 loop : -2.30 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.005 0.001 HIS B 580 PHE 0.041 0.001 PHE B 159 TYR 0.019 0.001 TYR B 79 ARG 0.003 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 113 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7838 (tt) REVERT: B 404 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: B 427 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5342 (pt0) REVERT: B 431 GLN cc_start: 0.6670 (pm20) cc_final: 0.6432 (pm20) REVERT: B 474 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6519 (mt-10) REVERT: B 695 ASN cc_start: 0.7216 (t0) cc_final: 0.6935 (t0) REVERT: A 364 THR cc_start: 0.4617 (OUTLIER) cc_final: 0.4297 (m) REVERT: A 450 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6155 (pp) REVERT: A 499 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 667 MET cc_start: 0.7069 (ttp) cc_final: 0.6776 (ttp) REVERT: A 668 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7219 (tttt) outliers start: 59 outliers final: 40 residues processed: 166 average time/residue: 0.2311 time to fit residues: 58.9244 Evaluate side-chains 148 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 0.0980 chunk 105 optimal weight: 0.3980 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12994 Z= 0.280 Angle : 0.747 11.250 17512 Z= 0.379 Chirality : 0.046 0.186 1998 Planarity : 0.004 0.049 2242 Dihedral : 5.375 24.211 1680 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.28 % Favored : 88.48 % Rotamer: Outliers : 3.79 % Allowed : 28.00 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.20), residues: 1614 helix: -0.86 (0.19), residues: 672 sheet: -0.70 (0.50), residues: 128 loop : -2.25 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.006 0.001 HIS B 580 PHE 0.036 0.002 PHE B 159 TYR 0.016 0.001 TYR B 79 ARG 0.003 0.000 ARG B 548 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 359 PHE cc_start: 0.4887 (t80) cc_final: 0.4687 (t80) REVERT: B 404 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: B 431 GLN cc_start: 0.6745 (pm20) cc_final: 0.6492 (pm20) REVERT: B 453 ASN cc_start: 0.7498 (p0) cc_final: 0.7261 (p0) REVERT: B 474 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6826 (mt-10) REVERT: B 695 ASN cc_start: 0.7312 (t0) cc_final: 0.7025 (t0) REVERT: A 294 MET cc_start: 0.7675 (ptm) cc_final: 0.7307 (ptt) REVERT: A 364 THR cc_start: 0.4766 (OUTLIER) cc_final: 0.4339 (m) REVERT: A 450 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6153 (pp) REVERT: A 499 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (mt) REVERT: A 667 MET cc_start: 0.7108 (ttp) cc_final: 0.6829 (ttp) REVERT: A 668 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7134 (tttt) outliers start: 53 outliers final: 39 residues processed: 157 average time/residue: 0.2181 time to fit residues: 53.4030 Evaluate side-chains 147 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 361 ASN B 590 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.219738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.184624 restraints weight = 19193.535| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.42 r_work: 0.3937 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12994 Z= 0.209 Angle : 0.704 11.532 17512 Z= 0.358 Chirality : 0.044 0.204 1998 Planarity : 0.004 0.047 2242 Dihedral : 5.225 25.042 1680 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.29 % Favored : 89.47 % Rotamer: Outliers : 3.57 % Allowed : 28.50 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.20), residues: 1614 helix: -0.80 (0.19), residues: 686 sheet: -0.64 (0.50), residues: 128 loop : -2.27 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 121 HIS 0.005 0.001 HIS B 580 PHE 0.032 0.001 PHE B 159 TYR 0.019 0.001 TYR A 740 ARG 0.003 0.000 ARG B 548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3024.30 seconds wall clock time: 57 minutes 4.63 seconds (3424.63 seconds total)