Starting phenix.real_space_refine on Mon Aug 25 06:21:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tbg_25798/08_2025/7tbg_25798.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tbg_25798/08_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_25798/08_2025/7tbg_25798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tbg_25798/08_2025/7tbg_25798.map" model { file = "/net/cci-nas-00/data/ceres_data/7tbg_25798/08_2025/7tbg_25798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tbg_25798/08_2025/7tbg_25798.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.09, per 1000 atoms: 0.21 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: 1.42 Conformation dependent library (CDL) restraints added in 442.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.41 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: 4.35 Time building geometry restraints manager: 2.13 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 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: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.120 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.820 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.770 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.003 ARG B 279 TYR 0.026 0.006 TYR A 608 PHE 0.021 0.003 PHE B 599 TRP 0.027 0.004 TRP A 271 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00605 (10052) covalent geometry : angle 0.75895 (13662) SS BOND : bond 0.00551 ( 2) SS BOND : angle 1.81178 ( 4) hydrogen bonds : bond 0.12627 ( 682) hydrogen bonds : angle 5.91214 ( 1998) *********************** 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 : 0.389 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: 0.6515 (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: 1.3351 time to fit residues: 394.9658 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 : 0.554 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.141645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113551 restraints weight = 35697.781| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.61 r_work: 0.3333 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10054 Z= 0.245 Angle : 0.622 5.908 13666 Z= 0.341 Chirality : 0.042 0.153 1554 Planarity : 0.005 0.049 1670 Dihedral : 5.144 28.316 1297 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.36 % Allowed : 11.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.25), residues: 1166 helix: 1.24 (0.17), residues: 878 sheet: None (None), residues: 0 loop : 1.40 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 537 TYR 0.026 0.002 TYR B 141 PHE 0.021 0.002 PHE B 599 TRP 0.019 0.002 TRP A 271 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00581 (10052) covalent geometry : angle 0.62190 (13662) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.07417 ( 4) hydrogen bonds : bond 0.06699 ( 682) hydrogen bonds : angle 4.91145 ( 1998) *********************** 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 251 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7443 (t0) cc_final: 0.7060 (t0) REVERT: A 69 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7458 (ttm170) REVERT: A 343 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7333 (p0) REVERT: A 399 PHE cc_start: 0.6113 (t80) cc_final: 0.5723 (t80) REVERT: A 560 THR cc_start: 0.8569 (t) cc_final: 0.8342 (p) REVERT: A 629 MET cc_start: 0.8824 (mmm) cc_final: 0.8552 (mmp) REVERT: A 681 LEU cc_start: 0.8430 (tt) cc_final: 0.8179 (tp) REVERT: A 683 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6762 (tm-30) REVERT: B 166 ASP cc_start: 0.7568 (m-30) cc_final: 0.7295 (m-30) REVERT: B 225 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8570 (mp) REVERT: B 540 ARG cc_start: 0.7201 (ttp80) cc_final: 0.6998 (ttp-110) REVERT: B 629 MET cc_start: 0.8859 (mmm) cc_final: 0.8606 (mmp) outliers start: 25 outliers final: 12 residues processed: 235 average time/residue: 1.4340 time to fit residues: 359.1917 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 : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 66 ILE 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 343 ASP 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 169 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 225 LEU 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 68 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.140664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112996 restraints weight = 35762.619| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.60 r_work: 0.3349 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10054 Z= 0.179 Angle : 0.543 5.075 13666 Z= 0.296 Chirality : 0.038 0.140 1554 Planarity : 0.004 0.048 1670 Dihedral : 4.787 26.959 1297 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 12.83 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.25), residues: 1166 helix: 1.57 (0.17), residues: 876 sheet: None (None), residues: 0 loop : 1.46 (0.43), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 537 TYR 0.022 0.002 TYR B 141 PHE 0.017 0.001 PHE B 599 TRP 0.013 0.001 TRP B 271 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00417 (10052) covalent geometry : angle 0.54269 (13662) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.82160 ( 4) hydrogen bonds : bond 0.05921 ( 682) hydrogen bonds : angle 4.61338 ( 1998) *********************** 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 262 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.531 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 23 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 43 ASP cc_start: 0.7477 (t0) cc_final: 0.7055 (t0) REVERT: A 69 ARG cc_start: 0.7685 (ttm170) cc_final: 0.7425 (ttm170) REVERT: A 78 TYR cc_start: 0.7934 (m-80) cc_final: 0.7343 (m-10) REVERT: A 399 PHE cc_start: 0.6196 (t80) cc_final: 0.5731 (t80) REVERT: A 629 MET cc_start: 0.8791 (mmm) cc_final: 0.8499 (mmp) REVERT: A 681 LEU cc_start: 0.8451 (tt) cc_final: 0.8202 (tp) REVERT: A 683 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6843 (tm-30) REVERT: B 147 PHE cc_start: 0.8135 (t80) cc_final: 0.7722 (t80) REVERT: B 166 ASP cc_start: 0.7547 (m-30) cc_final: 0.7265 (m-30) REVERT: B 225 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8589 (mp) REVERT: B 324 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7210 (mtp85) REVERT: B 328 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: B 629 MET cc_start: 0.8842 (mmm) cc_final: 0.8528 (mmp) outliers start: 26 outliers final: 11 residues processed: 243 average time/residue: 1.5468 time to fit residues: 399.4252 Evaluate side-chains 241 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE 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 391 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 185 ARG Chi-restraints excluded: chain B residue 222 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 75 optimal weight: 0.0980 chunk 108 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.141761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113741 restraints weight = 35498.223| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.65 r_work: 0.3361 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10054 Z= 0.143 Angle : 0.511 5.365 13666 Z= 0.279 Chirality : 0.036 0.135 1554 Planarity : 0.004 0.048 1670 Dihedral : 4.477 21.684 1296 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.70 % Allowed : 13.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.25), residues: 1166 helix: 1.74 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 1.52 (0.45), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 200 TYR 0.020 0.001 TYR B 141 PHE 0.015 0.001 PHE A 195 TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00318 (10052) covalent geometry : angle 0.51092 (13662) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.69484 ( 4) hydrogen bonds : bond 0.05384 ( 682) hydrogen bonds : angle 4.45576 ( 1998) *********************** 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 253 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 0.574 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 23 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 43 ASP cc_start: 0.7517 (t0) cc_final: 0.7080 (t0) REVERT: A 69 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7448 (ttm170) REVERT: A 78 TYR cc_start: 0.7937 (m-80) cc_final: 0.7357 (m-10) REVERT: A 399 PHE cc_start: 0.6026 (t80) cc_final: 0.5526 (t80) REVERT: A 629 MET cc_start: 0.8767 (mmm) cc_final: 0.8502 (mmp) REVERT: A 681 LEU cc_start: 0.8445 (tt) cc_final: 0.8212 (tp) REVERT: B 147 PHE cc_start: 0.8187 (t80) cc_final: 0.7752 (t80) REVERT: B 166 ASP cc_start: 0.7573 (m-30) cc_final: 0.7280 (m-30) REVERT: B 225 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 328 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 629 MET cc_start: 0.8831 (mmm) cc_final: 0.8554 (mmp) outliers start: 18 outliers final: 9 residues processed: 242 average time/residue: 1.5396 time to fit residues: 395.7475 Evaluate side-chains 240 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 102 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.139432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111807 restraints weight = 35503.703| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.58 r_work: 0.3335 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3192 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= 0.214 Angle : 0.542 5.739 13666 Z= 0.296 Chirality : 0.039 0.147 1554 Planarity : 0.005 0.054 1670 Dihedral : 4.523 22.767 1296 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.98 % Allowed : 13.96 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.25), residues: 1166 helix: 1.70 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 1.36 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 200 TYR 0.026 0.002 TYR B 141 PHE 0.019 0.002 PHE A 147 TRP 0.010 0.001 TRP A 271 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00509 (10052) covalent geometry : angle 0.54219 (13662) SS BOND : bond 0.00218 ( 2) SS BOND : angle 0.89014 ( 4) hydrogen bonds : bond 0.05931 ( 682) hydrogen bonds : angle 4.47379 ( 1998) *********************** 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 243 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.569 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: A 23 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 43 ASP cc_start: 0.7470 (t0) cc_final: 0.7169 (t70) REVERT: A 78 TYR cc_start: 0.7935 (m-80) cc_final: 0.7387 (m-10) REVERT: A 399 PHE cc_start: 0.6095 (t80) cc_final: 0.5546 (t80) REVERT: A 629 MET cc_start: 0.8764 (mmm) cc_final: 0.8478 (mmp) REVERT: A 681 LEU cc_start: 0.8474 (tt) cc_final: 0.8214 (tp) REVERT: B 147 PHE cc_start: 0.8210 (t80) cc_final: 0.7818 (t80) REVERT: B 162 ILE cc_start: 0.8623 (mt) cc_final: 0.8360 (mt) REVERT: B 166 ASP cc_start: 0.7529 (m-30) cc_final: 0.7246 (m-30) REVERT: B 225 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 324 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7201 (mtp85) REVERT: B 328 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 560 THR cc_start: 0.8556 (t) cc_final: 0.8307 (p) REVERT: B 629 MET cc_start: 0.8765 (mmm) cc_final: 0.8483 (mmp) outliers start: 21 outliers final: 14 residues processed: 229 average time/residue: 1.6157 time to fit residues: 391.8157 Evaluate side-chains 239 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 224 MET 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 395 ILE Chi-restraints excluded: chain B residue 538 MET 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 97 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.139669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112567 restraints weight = 35532.318| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.56 r_work: 0.3337 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10054 Z= 0.219 Angle : 0.539 5.827 13666 Z= 0.295 Chirality : 0.039 0.148 1554 Planarity : 0.005 0.057 1670 Dihedral : 4.504 23.209 1296 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.45 % Allowed : 13.87 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.25), residues: 1166 helix: 1.61 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.99 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 200 TYR 0.024 0.002 TYR B 141 PHE 0.021 0.002 PHE A 147 TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00523 (10052) covalent geometry : angle 0.53883 (13662) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.88761 ( 4) hydrogen bonds : bond 0.05928 ( 682) hydrogen bonds : angle 4.46177 ( 1998) *********************** 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 254 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.537 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: 0.8060 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 43 ASP cc_start: 0.7461 (t0) cc_final: 0.7140 (t70) REVERT: A 78 TYR cc_start: 0.7936 (m-80) cc_final: 0.7452 (m-10) REVERT: A 399 PHE cc_start: 0.6121 (t80) cc_final: 0.5528 (t80) REVERT: A 560 THR cc_start: 0.8523 (t) cc_final: 0.8308 (p) REVERT: A 629 MET cc_start: 0.8734 (mmm) cc_final: 0.8459 (mmp) REVERT: A 681 LEU cc_start: 0.8469 (tt) cc_final: 0.8203 (tp) REVERT: B 147 PHE cc_start: 0.8227 (t80) cc_final: 0.7832 (t80) REVERT: B 162 ILE cc_start: 0.8606 (mt) cc_final: 0.8318 (mt) REVERT: B 166 ASP cc_start: 0.7520 (m-30) cc_final: 0.7230 (m-30) REVERT: B 225 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 324 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7194 (mtp85) REVERT: B 328 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: B 538 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5222 (ttp) REVERT: B 629 MET cc_start: 0.8727 (mmm) cc_final: 0.8471 (mmp) outliers start: 26 outliers final: 14 residues processed: 238 average time/residue: 1.5906 time to fit residues: 401.9031 Evaluate side-chains 240 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 224 MET Chi-restraints excluded: chain A residue 321 GLN 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 395 ILE 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 83 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112550 restraints weight = 35329.742| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.63 r_work: 0.3349 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10054 Z= 0.169 Angle : 0.512 5.475 13666 Z= 0.280 Chirality : 0.037 0.141 1554 Planarity : 0.004 0.057 1670 Dihedral : 4.378 21.596 1296 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.26 % Allowed : 14.34 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.25), residues: 1166 helix: 1.75 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.98 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 200 TYR 0.021 0.002 TYR B 141 PHE 0.021 0.001 PHE A 147 TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00391 (10052) covalent geometry : angle 0.51155 (13662) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.92904 ( 4) hydrogen bonds : bond 0.05537 ( 682) hydrogen bonds : angle 4.37997 ( 1998) *********************** 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: 24 poor density : 222 time to evaluate : 0.559 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: 0.8014 (mm-30) cc_final: 0.7585 (mm-30) REVERT: A 43 ASP cc_start: 0.7524 (t0) cc_final: 0.7183 (t70) REVERT: A 78 TYR cc_start: 0.7946 (m-80) cc_final: 0.7403 (m-10) REVERT: A 324 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7888 (mtp85) REVERT: A 399 PHE cc_start: 0.6042 (t80) cc_final: 0.5420 (t80) REVERT: A 494 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6413 (mt-10) REVERT: A 560 THR cc_start: 0.8531 (t) cc_final: 0.8272 (p) REVERT: A 629 MET cc_start: 0.8723 (mmm) cc_final: 0.8448 (mmp) REVERT: A 681 LEU cc_start: 0.8463 (tt) cc_final: 0.8193 (tp) REVERT: B 147 PHE cc_start: 0.8262 (t80) cc_final: 0.7854 (t80) REVERT: B 162 ILE cc_start: 0.8603 (mt) cc_final: 0.8309 (mt) REVERT: B 166 ASP cc_start: 0.7545 (m-30) cc_final: 0.7246 (m-30) REVERT: B 225 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8563 (mp) REVERT: B 324 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7245 (mtp85) REVERT: B 328 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: B 560 THR cc_start: 0.8539 (t) cc_final: 0.8303 (p) REVERT: B 629 MET cc_start: 0.8722 (mmm) cc_final: 0.8479 (mmp) outliers start: 24 outliers final: 11 residues processed: 229 average time/residue: 1.5978 time to fit residues: 388.3180 Evaluate side-chains 236 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 223 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 224 MET 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 395 ILE 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 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112126 restraints weight = 35629.597| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.59 r_work: 0.3340 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10054 Z= 0.193 Angle : 0.524 5.803 13666 Z= 0.286 Chirality : 0.038 0.145 1554 Planarity : 0.005 0.057 1670 Dihedral : 4.374 21.857 1296 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.36 % Allowed : 14.06 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.25), residues: 1166 helix: 1.75 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.90 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 428 TYR 0.023 0.002 TYR B 141 PHE 0.022 0.001 PHE A 147 TRP 0.009 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00457 (10052) covalent geometry : angle 0.52340 (13662) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.10465 ( 4) hydrogen bonds : bond 0.05667 ( 682) hydrogen bonds : angle 4.38763 ( 1998) *********************** 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: 25 poor density : 220 time to evaluate : 0.531 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 23 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7641 (mt-10) REVERT: A 43 ASP cc_start: 0.7446 (t0) cc_final: 0.7145 (t70) REVERT: A 78 TYR cc_start: 0.7939 (m-80) cc_final: 0.7384 (m-10) REVERT: A 494 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6421 (mt-10) REVERT: A 560 THR cc_start: 0.8531 (t) cc_final: 0.8272 (p) REVERT: A 629 MET cc_start: 0.8724 (mmm) cc_final: 0.8486 (mmp) REVERT: B 162 ILE cc_start: 0.8609 (mt) cc_final: 0.8315 (mt) REVERT: B 166 ASP cc_start: 0.7535 (m-30) cc_final: 0.7241 (m-30) REVERT: B 225 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 324 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7249 (mtp85) REVERT: B 328 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: B 629 MET cc_start: 0.8691 (mmm) cc_final: 0.8461 (mmp) outliers start: 25 outliers final: 15 residues processed: 231 average time/residue: 1.5657 time to fit residues: 384.4173 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 : 0.534 ------------------------------------------------------------------------------- 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 224 MET 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 219 ILE 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 352 GLU Chi-restraints excluded: chain B residue 395 ILE 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 99 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111637 restraints weight = 35478.964| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.58 r_work: 0.3332 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10054 Z= 0.217 Angle : 0.540 6.123 13666 Z= 0.294 Chirality : 0.039 0.148 1554 Planarity : 0.005 0.069 1670 Dihedral : 4.414 22.734 1296 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 14.34 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.25), residues: 1166 helix: 1.71 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.83 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 200 TYR 0.025 0.002 TYR B 141 PHE 0.023 0.002 PHE A 147 TRP 0.010 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00519 (10052) covalent geometry : angle 0.54013 (13662) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.07751 ( 4) hydrogen bonds : bond 0.05846 ( 682) hydrogen bonds : angle 4.40888 ( 1998) *********************** 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 247 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.533 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: 0.7970 (mm-30) cc_final: 0.7653 (mt-10) REVERT: A 43 ASP cc_start: 0.7428 (t0) cc_final: 0.7132 (t70) REVERT: A 78 TYR cc_start: 0.7955 (m-80) cc_final: 0.7468 (m-10) REVERT: A 494 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6405 (mt-10) REVERT: A 629 MET cc_start: 0.8709 (mmm) cc_final: 0.8457 (mmp) REVERT: B 162 ILE cc_start: 0.8622 (mt) cc_final: 0.8312 (mt) REVERT: B 166 ASP cc_start: 0.7529 (m-30) cc_final: 0.7237 (m-30) REVERT: B 225 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8550 (mp) REVERT: B 324 ARG cc_start: 0.7954 (mtp85) cc_final: 0.7232 (mtp85) REVERT: B 328 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: B 538 MET cc_start: 0.5565 (OUTLIER) cc_final: 0.5238 (ttp) REVERT: B 560 THR cc_start: 0.8538 (t) cc_final: 0.8320 (p) REVERT: B 629 MET cc_start: 0.8661 (mmm) cc_final: 0.8436 (mmp) outliers start: 23 outliers final: 15 residues processed: 233 average time/residue: 1.5573 time to fit residues: 386.0530 Evaluate side-chains 240 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 224 MET Chi-restraints excluded: chain A residue 321 GLN 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 219 ILE 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 395 ILE Chi-restraints excluded: chain B residue 538 MET 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 80 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.0070 chunk 43 optimal weight: 0.0670 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 315 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 = 0.140460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112844 restraints weight = 35652.762| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.59 r_work: 0.3346 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10054 Z= 0.152 Angle : 0.506 5.480 13666 Z= 0.277 Chirality : 0.036 0.138 1554 Planarity : 0.004 0.058 1670 Dihedral : 4.276 20.651 1296 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.89 % Allowed : 15.28 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.25), residues: 1166 helix: 1.85 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.89 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 200 TYR 0.020 0.001 TYR B 141 PHE 0.023 0.001 PHE A 147 TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00347 (10052) covalent geometry : angle 0.50633 (13662) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.85362 ( 4) hydrogen bonds : bond 0.05321 ( 682) hydrogen bonds : angle 4.32184 ( 1998) ********************** 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: 20 poor density : 223 time to evaluate : 0.548 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: 0.7934 (mm-30) cc_final: 0.7633 (mt-10) REVERT: A 43 ASP cc_start: 0.7412 (t0) cc_final: 0.7109 (t70) REVERT: A 78 TYR cc_start: 0.7931 (m-80) cc_final: 0.7384 (m-10) REVERT: A 494 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6382 (mt-10) REVERT: A 629 MET cc_start: 0.8687 (mmm) cc_final: 0.8434 (mmp) REVERT: B 147 PHE cc_start: 0.8126 (t80) cc_final: 0.7802 (t80) REVERT: B 162 ILE cc_start: 0.8590 (mt) cc_final: 0.8273 (mt) REVERT: B 166 ASP cc_start: 0.7534 (m-30) cc_final: 0.7232 (m-30) REVERT: B 225 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 324 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7243 (mtp85) REVERT: B 328 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: B 560 THR cc_start: 0.8542 (t) cc_final: 0.8294 (p) REVERT: B 629 MET cc_start: 0.8654 (mmm) cc_final: 0.8443 (mmp) outliers start: 20 outliers final: 14 residues processed: 228 average time/residue: 1.5991 time to fit residues: 387.3508 Evaluate side-chains 239 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 328 GLU 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 219 ILE 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 395 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113048 restraints weight = 35562.251| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.57 r_work: 0.3348 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10054 Z= 0.153 Angle : 0.506 5.454 13666 Z= 0.276 Chirality : 0.037 0.145 1554 Planarity : 0.005 0.058 1670 Dihedral : 4.236 19.982 1296 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.51 % Allowed : 16.13 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.25), residues: 1166 helix: 1.92 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.89 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 200 TYR 0.021 0.001 TYR B 141 PHE 0.023 0.001 PHE A 147 TRP 0.010 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00351 (10052) covalent geometry : angle 0.50561 (13662) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.81976 ( 4) hydrogen bonds : bond 0.05272 ( 682) hydrogen bonds : angle 4.29539 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9493.54 seconds wall clock time: 161 minutes 13.85 seconds (9673.85 seconds total)