Starting phenix.real_space_refine on Sun Jun 22 11:39:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tbg_25798/06_2025/7tbg_25798.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tbg_25798/06_2025/7tbg_25798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tbg_25798/06_2025/7tbg_25798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tbg_25798/06_2025/7tbg_25798.map" model { file = "/net/cci-nas-00/data/ceres_data/7tbg_25798/06_2025/7tbg_25798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tbg_25798/06_2025/7tbg_25798.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7528 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 S 44 5.16 5 Na 1 4.78 5 C 6532 2.51 5 N 1510 2.21 5 O 1730 1.98 5 H 9858 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19679 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9807 Classifications: {'peptide': 595} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9807 Classifications: {'peptide': 595} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 36 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 9.87, per 1000 atoms: 0.50 Number of scatterers: 19679 At special positions: 0 Unit cell: (111.055, 86.005, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 44 16.00 Na 1 11.00 O 1730 8.00 N 1510 7.00 C 6532 6.00 H 9858 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 101 " distance=2.04 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: 4.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.811A pdb=" N GLU A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.609A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.578A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 172 removed outlier: 3.980A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.549A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 3.552A pdb=" N GLY A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.224A pdb=" N PHE A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.798A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.987A pdb=" N GLY A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 487 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.881A pdb=" N PHE A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.870A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.719A pdb=" N ALA A 553 " --> pdb=" O GLN A 549 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.776A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 4.165A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 686 Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 56 through 70 removed outlier: 4.306A pdb=" N SER B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.562A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 150 through 172 removed outlier: 3.653A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.503A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 238 removed outlier: 3.604A pdb=" N MET B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.559A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.202A pdb=" N PHE B 284 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 335 Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.665A pdb=" N LYS B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.765A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 452 removed outlier: 4.247A pdb=" N GLY B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 487 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 511 removed outlier: 3.980A pdb=" N PHE B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.549A pdb=" N LEU B 533 " --> pdb=" O TRP B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 548 through 565 removed outlier: 4.613A pdb=" N ALA B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N PHE B 554 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 565 through 588 Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.760A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 4.137A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 686 682 hydrogen bonds defined for protein. 1998 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: 6.50 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9846 1.02 - 1.22: 12 1.22 - 1.42: 4376 1.42 - 1.62: 5604 1.62 - 1.82: 72 Bond restraints: 19910 Sorted by residual: bond pdb=" ND2 ASN B 631 " pdb="HD22 ASN B 631 " ideal model delta sigma weight residual 0.860 0.819 0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" CB PRO A 99 " pdb=" CG PRO A 99 " ideal model delta sigma weight residual 1.506 1.437 0.069 3.90e-02 6.57e+02 3.16e+00 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.506 1.439 0.067 3.90e-02 6.57e+02 2.95e+00 bond pdb=" N ARG A 20 " pdb=" CA ARG A 20 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" N ARG B 20 " pdb=" CA ARG B 20 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.53e+00 ... (remaining 19905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34638 1.64 - 3.27: 1117 3.27 - 4.91: 78 4.91 - 6.55: 12 6.55 - 8.18: 3 Bond angle restraints: 35848 Sorted by residual: angle pdb=" N ASN B 96 " pdb=" CA ASN B 96 " pdb=" C ASN B 96 " ideal model delta sigma weight residual 109.81 116.42 -6.61 2.21e+00 2.05e-01 8.94e+00 angle pdb=" CA TRP B 271 " pdb=" CB TRP B 271 " pdb=" CG TRP B 271 " ideal model delta sigma weight residual 113.60 119.25 -5.65 1.90e+00 2.77e-01 8.86e+00 angle pdb=" CA TRP A 271 " pdb=" CB TRP A 271 " pdb=" CG TRP A 271 " ideal model delta sigma weight residual 113.60 119.14 -5.54 1.90e+00 2.77e-01 8.49e+00 angle pdb=" N ASN A 96 " pdb=" CA ASN A 96 " pdb=" C ASN A 96 " ideal model delta sigma weight residual 109.81 115.84 -6.03 2.21e+00 2.05e-01 7.44e+00 angle pdb="HD21 ASN B 631 " pdb=" ND2 ASN B 631 " pdb="HD22 ASN B 631 " ideal model delta sigma weight residual 120.00 111.82 8.18 3.00e+00 1.11e-01 7.44e+00 ... (remaining 35843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8579 17.87 - 35.74: 462 35.74 - 53.61: 141 53.61 - 71.48: 156 71.48 - 89.35: 6 Dihedral angle restraints: 9344 sinusoidal: 4854 harmonic: 4490 Sorted by residual: dihedral pdb=" CA GLU B 600 " pdb=" C GLU B 600 " pdb=" N THR B 601 " pdb=" CA THR B 601 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG A 20 " pdb=" C ARG A 20 " pdb=" N ARG A 21 " pdb=" CA ARG A 21 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU A 600 " pdb=" C GLU A 600 " pdb=" N THR A 601 " pdb=" CA THR A 601 " ideal model delta harmonic sigma weight residual 180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 9341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 845 0.035 - 0.069: 527 0.069 - 0.104: 126 0.104 - 0.139: 43 0.139 - 0.173: 13 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA TRP B 271 " pdb=" N TRP B 271 " pdb=" C TRP B 271 " pdb=" CB TRP B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA PRO B 30 " pdb=" N PRO B 30 " pdb=" C PRO B 30 " pdb=" CB PRO B 30 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA GLU A 42 " pdb=" N GLU A 42 " pdb=" C GLU A 42 " pdb=" CB GLU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1551 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 631 " -0.064 2.00e-02 2.50e+03 8.18e-02 1.00e+02 pdb=" CG ASN B 631 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 631 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 631 " 0.130 2.00e-02 2.50e+03 pdb="HD21 ASN B 631 " 0.013 2.00e-02 2.50e+03 pdb="HD22 ASN B 631 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 631 " -0.052 2.00e-02 2.50e+03 6.58e-02 6.49e+01 pdb=" CG ASN A 631 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 631 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 631 " 0.105 2.00e-02 2.50e+03 pdb="HD21 ASN A 631 " 0.006 2.00e-02 2.50e+03 pdb="HD22 ASN A 631 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 191 " 0.227 9.50e-02 1.11e+02 7.99e-02 2.04e+01 pdb=" NE ARG B 191 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 191 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 191 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG B 191 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B 191 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 191 " 0.032 2.00e-02 2.50e+03 pdb="HH21 ARG B 191 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 191 " 0.034 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 645 2.14 - 2.76: 36495 2.76 - 3.37: 56344 3.37 - 3.99: 70418 3.99 - 4.60: 110815 Nonbonded interactions: 274717 Sorted by model distance: nonbonded pdb=" O THR A 263 " pdb=" HG1 THR A 264 " model vdw 1.526 2.450 nonbonded pdb=" HG1 THR B 452 " pdb=" OD1 ASN B 454 " model vdw 1.582 2.450 nonbonded pdb=" O TYR B 491 " pdb="HD22 ASN B 497 " model vdw 1.584 2.450 nonbonded pdb=" HG1 THR A 452 " pdb=" OD1 ASN A 454 " model vdw 1.588 2.450 nonbonded pdb=" O THR B 263 " pdb=" HG1 THR B 264 " model vdw 1.598 2.450 ... (remaining 274712 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' and (resid 20 through 686 or resid 801 through 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.310 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.750 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.006 0.069 10054 Z= 0.262 Angle : 0.759 6.607 13666 Z= 0.471 Chirality : 0.047 0.173 1554 Planarity : 0.009 0.133 1670 Dihedral : 13.033 89.345 3526 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.57 % Allowed : 4.53 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1166 helix: 0.18 (0.16), residues: 862 sheet: None (None), residues: 0 loop : 1.66 (0.44), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 271 HIS 0.004 0.001 HIS A 134 PHE 0.021 0.003 PHE B 599 TYR 0.026 0.006 TYR A 608 ARG 0.018 0.003 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.12627 ( 682) hydrogen bonds : angle 5.91214 ( 1998) SS BOND : bond 0.00551 ( 2) SS BOND : angle 1.81178 ( 4) covalent geometry : bond 0.00605 (10052) covalent geometry : angle 0.75895 (13662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 274 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.6807 (t0) cc_final: 0.6516 (t0) REVERT: A 399 PHE cc_start: 0.5522 (t80) cc_final: 0.5289 (t80) REVERT: A 629 MET cc_start: 0.8585 (mmm) cc_final: 0.8217 (mmp) REVERT: A 681 LEU cc_start: 0.8463 (tt) cc_final: 0.8254 (tp) REVERT: A 683 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6497 (tm-30) REVERT: B 147 PHE cc_start: 0.8078 (t80) cc_final: 0.7768 (t80) REVERT: B 629 MET cc_start: 0.8561 (mmm) cc_final: 0.8352 (mmp) outliers start: 6 outliers final: 2 residues processed: 278 average time/residue: 2.8298 time to fit residues: 839.6080 Evaluate side-chains 221 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114832 restraints weight = 35576.135| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.61 r_work: 0.3349 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10054 Z= 0.179 Angle : 0.585 5.858 13666 Z= 0.321 Chirality : 0.039 0.145 1554 Planarity : 0.005 0.049 1670 Dihedral : 5.008 27.133 1297 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 11.79 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.99 (0.25), residues: 1166 helix: 1.37 (0.17), residues: 878 sheet: None (None), residues: 0 loop : 1.53 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 271 HIS 0.003 0.001 HIS A 134 PHE 0.017 0.002 PHE A 554 TYR 0.021 0.002 TYR B 141 ARG 0.008 0.001 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.06175 ( 682) hydrogen bonds : angle 4.83357 ( 1998) SS BOND : bond 0.00099 ( 2) SS BOND : angle 1.06436 ( 4) covalent geometry : bond 0.00401 (10052) covalent geometry : angle 0.58495 (13662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7448 (t0) cc_final: 0.7061 (t0) REVERT: A 69 ARG cc_start: 0.7632 (ttm170) cc_final: 0.7379 (ttm170) REVERT: A 320 ASP cc_start: 0.7694 (m-30) cc_final: 0.7494 (m-30) REVERT: A 399 PHE cc_start: 0.6102 (t80) cc_final: 0.5713 (t80) REVERT: A 629 MET cc_start: 0.8827 (mmm) cc_final: 0.8553 (mmp) REVERT: A 681 LEU cc_start: 0.8402 (tt) cc_final: 0.8158 (tp) REVERT: A 683 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6747 (tm-30) REVERT: B 147 PHE cc_start: 0.8244 (t80) cc_final: 0.7737 (t80) REVERT: B 166 ASP cc_start: 0.7574 (m-30) cc_final: 0.7301 (m-30) REVERT: B 225 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8552 (mp) REVERT: B 629 MET cc_start: 0.8843 (mmm) cc_final: 0.8497 (mmp) outliers start: 23 outliers final: 12 residues processed: 229 average time/residue: 2.9171 time to fit residues: 716.2383 Evaluate side-chains 240 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 227 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111936 restraints weight = 35438.250| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.59 r_work: 0.3336 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10054 Z= 0.222 Angle : 0.570 5.489 13666 Z= 0.311 Chirality : 0.040 0.146 1554 Planarity : 0.004 0.051 1670 Dihedral : 4.784 25.851 1296 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 12.92 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.11 (0.25), residues: 1166 helix: 1.49 (0.17), residues: 878 sheet: None (None), residues: 0 loop : 1.46 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 271 HIS 0.003 0.001 HIS B 134 PHE 0.021 0.002 PHE B 599 TYR 0.025 0.002 TYR B 141 ARG 0.006 0.000 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.06272 ( 682) hydrogen bonds : angle 4.66311 ( 1998) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.97607 ( 4) covalent geometry : bond 0.00528 (10052) covalent geometry : angle 0.56953 (13662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 43 ASP cc_start: 0.7465 (t0) cc_final: 0.7039 (t0) REVERT: A 69 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7431 (ttm170) REVERT: A 78 TYR cc_start: 0.7948 (m-80) cc_final: 0.7403 (m-10) REVERT: A 399 PHE cc_start: 0.6185 (t80) cc_final: 0.5736 (t80) REVERT: A 629 MET cc_start: 0.8784 (mmm) cc_final: 0.8571 (mmp) REVERT: A 681 LEU cc_start: 0.8485 (tt) cc_final: 0.8234 (tp) REVERT: A 683 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6841 (tm-30) REVERT: B 147 PHE cc_start: 0.8308 (t80) cc_final: 0.7837 (t80) REVERT: B 162 ILE cc_start: 0.8608 (mt) cc_final: 0.8359 (mt) REVERT: B 166 ASP cc_start: 0.7560 (m-30) cc_final: 0.7285 (m-30) REVERT: B 225 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8592 (mp) REVERT: B 560 THR cc_start: 0.8575 (t) cc_final: 0.8322 (p) REVERT: B 629 MET cc_start: 0.8854 (mmm) cc_final: 0.8533 (mmp) outliers start: 21 outliers final: 11 residues processed: 243 average time/residue: 2.9851 time to fit residues: 776.3806 Evaluate side-chains 242 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 230 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111356 restraints weight = 35896.396| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.59 r_work: 0.3327 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10054 Z= 0.226 Angle : 0.556 5.797 13666 Z= 0.304 Chirality : 0.039 0.148 1554 Planarity : 0.005 0.057 1670 Dihedral : 4.661 24.574 1296 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.55 % Allowed : 12.92 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.07 (0.25), residues: 1166 helix: 1.50 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 1.30 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 271 HIS 0.003 0.001 HIS B 134 PHE 0.020 0.002 PHE B 599 TYR 0.025 0.002 TYR B 141 ARG 0.005 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.06122 ( 682) hydrogen bonds : angle 4.57070 ( 1998) SS BOND : bond 0.00237 ( 2) SS BOND : angle 0.92124 ( 4) covalent geometry : bond 0.00539 (10052) covalent geometry : angle 0.55634 (13662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 43 ASP cc_start: 0.7493 (t0) cc_final: 0.7162 (t70) REVERT: A 69 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7390 (ttm170) REVERT: A 78 TYR cc_start: 0.7956 (m-80) cc_final: 0.7401 (m-10) REVERT: A 399 PHE cc_start: 0.6046 (t80) cc_final: 0.5517 (t80) REVERT: A 560 THR cc_start: 0.8556 (t) cc_final: 0.8289 (p) REVERT: A 629 MET cc_start: 0.8779 (mmm) cc_final: 0.8487 (mmp) REVERT: A 681 LEU cc_start: 0.8446 (tt) cc_final: 0.8189 (tp) REVERT: B 147 PHE cc_start: 0.8300 (t80) cc_final: 0.8033 (t80) REVERT: B 162 ILE cc_start: 0.8599 (mt) cc_final: 0.8331 (mt) REVERT: B 166 ASP cc_start: 0.7551 (m-30) cc_final: 0.7260 (m-30) REVERT: B 225 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 324 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7731 (mtp85) REVERT: B 326 MET cc_start: 0.8484 (mtp) cc_final: 0.8223 (mtt) outliers start: 27 outliers final: 16 residues processed: 238 average time/residue: 2.8603 time to fit residues: 726.6667 Evaluate side-chains 245 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 66 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.113347 restraints weight = 35503.537| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.60 r_work: 0.3351 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10054 Z= 0.147 Angle : 0.507 5.066 13666 Z= 0.277 Chirality : 0.036 0.136 1554 Planarity : 0.004 0.052 1670 Dihedral : 4.441 21.583 1296 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.26 % Allowed : 12.55 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.38 (0.25), residues: 1166 helix: 1.74 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 1.33 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 PHE 0.017 0.001 PHE A 147 TYR 0.020 0.001 TYR B 141 ARG 0.006 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.05428 ( 682) hydrogen bonds : angle 4.41828 ( 1998) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.83658 ( 4) covalent geometry : bond 0.00329 (10052) covalent geometry : angle 0.50698 (13662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 43 ASP cc_start: 0.7503 (t0) cc_final: 0.7175 (t70) REVERT: A 78 TYR cc_start: 0.7945 (m-80) cc_final: 0.7336 (m-10) REVERT: A 399 PHE cc_start: 0.5968 (t80) cc_final: 0.5407 (t80) REVERT: A 629 MET cc_start: 0.8753 (mmm) cc_final: 0.8488 (mmp) REVERT: A 681 LEU cc_start: 0.8420 (tt) cc_final: 0.8156 (tp) REVERT: B 162 ILE cc_start: 0.8588 (mt) cc_final: 0.8309 (mt) REVERT: B 166 ASP cc_start: 0.7555 (m-30) cc_final: 0.7253 (m-30) REVERT: B 225 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 326 MET cc_start: 0.8447 (mtp) cc_final: 0.8160 (mtt) REVERT: B 560 THR cc_start: 0.8567 (t) cc_final: 0.8321 (p) outliers start: 24 outliers final: 11 residues processed: 234 average time/residue: 3.1117 time to fit residues: 780.1410 Evaluate side-chains 234 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111799 restraints weight = 35578.871| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.57 r_work: 0.3336 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10054 Z= 0.204 Angle : 0.527 5.759 13666 Z= 0.289 Chirality : 0.038 0.145 1554 Planarity : 0.004 0.055 1670 Dihedral : 4.440 22.235 1296 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.26 % Allowed : 13.40 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.18 (0.25), residues: 1166 helix: 1.64 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 1.06 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 271 HIS 0.003 0.001 HIS B 134 PHE 0.020 0.002 PHE A 147 TYR 0.024 0.002 TYR B 141 ARG 0.007 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.05798 ( 682) hydrogen bonds : angle 4.42683 ( 1998) SS BOND : bond 0.00238 ( 2) SS BOND : angle 1.12862 ( 4) covalent geometry : bond 0.00484 (10052) covalent geometry : angle 0.52709 (13662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7712 (mt-10) REVERT: A 43 ASP cc_start: 0.7488 (t0) cc_final: 0.6940 (t0) REVERT: A 78 TYR cc_start: 0.7930 (m-80) cc_final: 0.7381 (m-10) REVERT: A 399 PHE cc_start: 0.6081 (t80) cc_final: 0.5491 (t80) REVERT: A 494 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6400 (mt-10) REVERT: A 560 THR cc_start: 0.8550 (t) cc_final: 0.8298 (p) REVERT: A 629 MET cc_start: 0.8728 (mmm) cc_final: 0.8450 (mmp) REVERT: B 162 ILE cc_start: 0.8603 (mt) cc_final: 0.8315 (mt) REVERT: B 166 ASP cc_start: 0.7518 (m-30) cc_final: 0.7224 (m-30) REVERT: B 225 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 324 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7694 (mtp85) REVERT: B 326 MET cc_start: 0.8490 (mtp) cc_final: 0.8193 (mtt) REVERT: B 538 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5224 (ttp) outliers start: 24 outliers final: 13 residues processed: 229 average time/residue: 3.0156 time to fit residues: 745.9571 Evaluate side-chains 237 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112407 restraints weight = 35306.822| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.59 r_work: 0.3337 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10054 Z= 0.191 Angle : 0.518 5.674 13666 Z= 0.284 Chirality : 0.038 0.144 1554 Planarity : 0.004 0.055 1670 Dihedral : 4.390 22.000 1296 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.89 % Allowed : 13.96 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.23 (0.25), residues: 1166 helix: 1.69 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 1.00 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 PHE 0.022 0.001 PHE A 147 TYR 0.022 0.002 TYR B 141 ARG 0.007 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.05679 ( 682) hydrogen bonds : angle 4.39400 ( 1998) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.95048 ( 4) covalent geometry : bond 0.00452 (10052) covalent geometry : angle 0.51817 (13662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7761 (mt-10) REVERT: A 43 ASP cc_start: 0.7511 (t0) cc_final: 0.7172 (t70) REVERT: A 78 TYR cc_start: 0.7927 (m-80) cc_final: 0.7368 (m-10) REVERT: A 399 PHE cc_start: 0.6029 (t80) cc_final: 0.5402 (t80) REVERT: A 629 MET cc_start: 0.8731 (mmm) cc_final: 0.8469 (mmp) REVERT: B 162 ILE cc_start: 0.8615 (mt) cc_final: 0.8320 (mt) REVERT: B 166 ASP cc_start: 0.7545 (m-30) cc_final: 0.7248 (m-30) REVERT: B 225 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 324 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7738 (mtp85) REVERT: B 326 MET cc_start: 0.8491 (mtp) cc_final: 0.8185 (mtt) REVERT: B 560 THR cc_start: 0.8552 (t) cc_final: 0.8312 (p) outliers start: 20 outliers final: 12 residues processed: 233 average time/residue: 2.8844 time to fit residues: 716.9814 Evaluate side-chains 235 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111589 restraints weight = 35646.216| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.58 r_work: 0.3330 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10054 Z= 0.210 Angle : 0.531 6.003 13666 Z= 0.290 Chirality : 0.038 0.147 1554 Planarity : 0.005 0.066 1670 Dihedral : 4.404 22.460 1296 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 14.53 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.19 (0.25), residues: 1166 helix: 1.68 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.90 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 PHE 0.023 0.002 PHE A 147 TYR 0.024 0.002 TYR B 141 ARG 0.010 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.05809 ( 682) hydrogen bonds : angle 4.41382 ( 1998) SS BOND : bond 0.00251 ( 2) SS BOND : angle 0.98934 ( 4) covalent geometry : bond 0.00499 (10052) covalent geometry : angle 0.53107 (13662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7677 (mt-10) REVERT: A 43 ASP cc_start: 0.7477 (t0) cc_final: 0.7160 (t70) REVERT: A 78 TYR cc_start: 0.7949 (m-80) cc_final: 0.7462 (m-10) REVERT: A 560 THR cc_start: 0.8536 (t) cc_final: 0.8300 (p) REVERT: A 629 MET cc_start: 0.8716 (mmm) cc_final: 0.8471 (mmp) REVERT: B 162 ILE cc_start: 0.8617 (mt) cc_final: 0.8311 (mt) REVERT: B 166 ASP cc_start: 0.7534 (m-30) cc_final: 0.7236 (m-30) REVERT: B 225 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8551 (mp) REVERT: B 323 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8159 (ttmm) REVERT: B 324 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7719 (mtp85) REVERT: B 326 MET cc_start: 0.8519 (mtp) cc_final: 0.8213 (mtt) outliers start: 23 outliers final: 15 residues processed: 229 average time/residue: 2.8165 time to fit residues: 688.8175 Evaluate side-chains 238 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111722 restraints weight = 35229.492| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.58 r_work: 0.3331 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10054 Z= 0.197 Angle : 0.526 5.934 13666 Z= 0.287 Chirality : 0.038 0.146 1554 Planarity : 0.005 0.055 1670 Dihedral : 4.369 22.261 1296 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.98 % Allowed : 14.81 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.23 (0.25), residues: 1166 helix: 1.72 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.88 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 PHE 0.022 0.001 PHE A 147 TYR 0.023 0.002 TYR B 141 ARG 0.008 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.05706 ( 682) hydrogen bonds : angle 4.39227 ( 1998) SS BOND : bond 0.00209 ( 2) SS BOND : angle 0.94754 ( 4) covalent geometry : bond 0.00468 (10052) covalent geometry : angle 0.52547 (13662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7694 (mt-10) REVERT: A 43 ASP cc_start: 0.7460 (t0) cc_final: 0.7143 (t70) REVERT: A 78 TYR cc_start: 0.7947 (m-80) cc_final: 0.7388 (m-10) REVERT: A 560 THR cc_start: 0.8545 (t) cc_final: 0.8290 (p) REVERT: A 629 MET cc_start: 0.8707 (mmm) cc_final: 0.8467 (mmp) REVERT: B 162 ILE cc_start: 0.8614 (mt) cc_final: 0.8301 (mt) REVERT: B 166 ASP cc_start: 0.7540 (m-30) cc_final: 0.7240 (m-30) REVERT: B 225 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 323 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8167 (ttmm) REVERT: B 324 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7737 (mtp85) REVERT: B 326 MET cc_start: 0.8523 (mtp) cc_final: 0.8216 (mtt) REVERT: B 560 THR cc_start: 0.8562 (t) cc_final: 0.8327 (p) outliers start: 21 outliers final: 16 residues processed: 229 average time/residue: 2.7427 time to fit residues: 671.1881 Evaluate side-chains 241 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 0.0370 chunk 114 optimal weight: 0.8980 chunk 62 optimal weight: 0.0370 chunk 73 optimal weight: 0.9990 chunk 116 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 93 optimal weight: 0.3980 overall best weight: 0.1274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.143531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116146 restraints weight = 35308.362| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.57 r_work: 0.3389 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10054 Z= 0.107 Angle : 0.472 4.172 13666 Z= 0.257 Chirality : 0.035 0.124 1554 Planarity : 0.004 0.050 1670 Dihedral : 4.067 16.400 1296 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.32 % Allowed : 15.38 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.73 (0.25), residues: 1166 helix: 2.06 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 1.15 (0.46), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.021 0.001 PHE A 147 TYR 0.015 0.001 TYR B 141 ARG 0.009 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 682) hydrogen bonds : angle 4.16461 ( 1998) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.56103 ( 4) covalent geometry : bond 0.00220 (10052) covalent geometry : angle 0.47206 (13662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7607 (mt-10) REVERT: A 43 ASP cc_start: 0.7399 (t0) cc_final: 0.7092 (t70) REVERT: A 78 TYR cc_start: 0.7915 (m-80) cc_final: 0.7267 (m-10) REVERT: A 560 THR cc_start: 0.8528 (t) cc_final: 0.8315 (p) REVERT: A 629 MET cc_start: 0.8681 (mmm) cc_final: 0.8406 (mmp) REVERT: B 162 ILE cc_start: 0.8584 (mt) cc_final: 0.8267 (mt) REVERT: B 166 ASP cc_start: 0.7524 (m-30) cc_final: 0.7226 (m-30) REVERT: B 225 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8506 (mp) REVERT: B 323 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8160 (ttmm) REVERT: B 326 MET cc_start: 0.8411 (mtp) cc_final: 0.8095 (mtt) REVERT: B 560 THR cc_start: 0.8548 (t) cc_final: 0.8343 (p) outliers start: 14 outliers final: 10 residues processed: 233 average time/residue: 2.8673 time to fit residues: 712.9476 Evaluate side-chains 239 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 562 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 116 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113078 restraints weight = 35505.369| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.59 r_work: 0.3347 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10054 Z= 0.173 Angle : 0.518 5.670 13666 Z= 0.281 Chirality : 0.037 0.139 1554 Planarity : 0.005 0.073 1670 Dihedral : 4.179 18.335 1296 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.13 % Allowed : 16.79 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.25), residues: 1166 helix: 2.00 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 1.03 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.003 0.001 HIS B 134 PHE 0.023 0.001 PHE A 147 TYR 0.023 0.002 TYR B 141 ARG 0.011 0.001 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.05272 ( 682) hydrogen bonds : angle 4.27005 ( 1998) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.87925 ( 4) covalent geometry : bond 0.00404 (10052) covalent geometry : angle 0.51827 (13662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18814.59 seconds wall clock time: 322 minutes 26.48 seconds (19346.48 seconds total)