Starting phenix.real_space_refine on Tue Aug 4 16:17:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wla_66051/08_2026/9wla_66051.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wla_66051/08_2026/9wla_66051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wla_66051/08_2026/9wla_66051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wla_66051/08_2026/9wla_66051.map" model { file = "/net/cci-nas-00/data/ceres_data/9wla_66051/08_2026/9wla_66051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wla_66051/08_2026/9wla_66051.cif" } resolution = 3.6 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= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 Cl 1 4.86 5 C 2985 2.51 5 N 797 2.21 5 O 864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4669 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 758 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 938 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1506 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 782 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 684 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.17, per 1000 atoms: 0.25 Number of scatterers: 4669 At special positions: 0 Unit cell: (72.15, 105.3, 105.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 22 16.00 O 864 8.00 N 797 7.00 C 2985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.17 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.05 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.11 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.22 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: 0.36 Conformation dependent library (CDL) restraints added in 165.2 milliseconds 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 16 sheets defined 9.0% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.592A pdb=" N SER D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.265A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 371 removed outlier: 3.919A pdb=" N SER R 371 " --> pdb=" O VAL R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 386 through 390 removed outlier: 3.861A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 416 through 422 removed outlier: 3.546A pdb=" N ASP R 420 " --> pdb=" O GLY R 416 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.774A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.923A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 29 removed outlier: 12.339A pdb=" N CYS B 23 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N THR B 75 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 12.185A pdb=" N ALA B 25 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 12.035A pdb=" N THR B 73 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 11.704A pdb=" N GLN B 27 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 71 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 69 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.521A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.665A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 33 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.665A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS D 96 " --> pdb=" O TRP D 117 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TRP D 117 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 98 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.509A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA R 435 " --> pdb=" O SER R 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.509A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 removed outlier: 3.705A pdb=" N TYR R 453 " --> pdb=" O GLN R 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.518A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.576A pdb=" N ALA H 97 " --> pdb=" O GLN H 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.576A pdb=" N ALA H 97 " --> pdb=" O GLN H 35 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB7, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.581A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA L 35 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 369 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: 0.40 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.35: 1499 1.35 - 1.51: 1520 1.51 - 1.67: 1742 1.67 - 1.83: 26 Bond restraints: 4788 Sorted by residual: bond pdb=" CG PRO R 521 " pdb=" CD PRO R 521 " ideal model delta sigma weight residual 1.503 1.022 0.481 3.40e-02 8.65e+02 2.00e+02 bond pdb=" N ILE H 70 " pdb=" CA ILE H 70 " ideal model delta sigma weight residual 1.458 1.506 -0.047 1.17e-02 7.31e+03 1.64e+01 bond pdb=" N PRO R 521 " pdb=" CD PRO R 521 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB PRO R 521 " pdb=" CG PRO R 521 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.18e+01 bond pdb=" C CYS R 525 " pdb=" O CYS R 525 " ideal model delta sigma weight residual 1.236 1.204 0.032 9.60e-03 1.09e+04 1.08e+01 ... (remaining 4783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 6536 4.92 - 9.84: 6 9.84 - 14.77: 0 14.77 - 19.69: 0 19.69 - 24.61: 2 Bond angle restraints: 6544 Sorted by residual: angle pdb=" N PRO R 521 " pdb=" CD PRO R 521 " pdb=" CG PRO R 521 " ideal model delta sigma weight residual 103.20 78.59 24.61 1.50e+00 4.44e-01 2.69e+02 angle pdb=" CA PRO R 521 " pdb=" CB PRO R 521 " pdb=" CG PRO R 521 " ideal model delta sigma weight residual 104.50 84.75 19.75 1.90e+00 2.77e-01 1.08e+02 angle pdb=" N PRO R 521 " pdb=" CA PRO R 521 " pdb=" CB PRO R 521 " ideal model delta sigma weight residual 103.25 95.70 7.55 1.05e+00 9.07e-01 5.17e+01 angle pdb=" CA GLY R 431 " pdb=" C GLY R 431 " pdb=" O GLY R 431 " ideal model delta sigma weight residual 122.52 119.01 3.51 7.90e-01 1.60e+00 1.98e+01 angle pdb=" N ASP R 389 " pdb=" CA ASP R 389 " pdb=" CB ASP R 389 " ideal model delta sigma weight residual 111.00 105.45 5.55 1.33e+00 5.65e-01 1.74e+01 ... (remaining 6539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 2446 15.72 - 31.44: 229 31.44 - 47.16: 58 47.16 - 62.87: 10 62.87 - 78.59: 4 Dihedral angle restraints: 2747 sinusoidal: 914 harmonic: 1833 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 154.53 -61.53 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CD ARG H 72 " pdb=" NE ARG H 72 " pdb=" CZ ARG H 72 " pdb=" NH1 ARG H 72 " ideal model delta sinusoidal sigma weight residual 0.00 57.48 -57.48 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 41.10 51.90 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 2744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 464 0.034 - 0.067: 150 0.067 - 0.101: 74 0.101 - 0.135: 32 0.135 - 0.168: 5 Chirality restraints: 725 Sorted by residual: chirality pdb=" CB THR L 10 " pdb=" CA THR L 10 " pdb=" OG1 THR L 10 " pdb=" CG2 THR L 10 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CB THR L 57 " pdb=" CA THR L 57 " pdb=" OG1 THR L 57 " pdb=" CG2 THR L 57 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE B 106 " pdb=" N ILE B 106 " pdb=" C ILE B 106 " pdb=" CB ILE B 106 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 722 not shown) Planarity restraints: 845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 72 " -0.929 9.50e-02 1.11e+02 4.16e-01 1.05e+02 pdb=" NE ARG H 72 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG H 72 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG H 72 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 72 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 83 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ASP B 83 " -0.058 2.00e-02 2.50e+03 pdb=" O ASP B 83 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE B 84 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 389 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C ASP R 389 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP R 389 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 390 " -0.017 2.00e-02 2.50e+03 ... (remaining 842 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 591 2.75 - 3.29: 4204 3.29 - 3.83: 7258 3.83 - 4.36: 8506 4.36 - 4.90: 15158 Nonbonded interactions: 35717 Sorted by model distance: nonbonded pdb=" OG SER D 35 " pdb=" OD2 ASP D 99 " model vdw 2.218 3.040 nonbonded pdb=" OG SER D 52 " pdb=" O ALA D 104 " model vdw 2.299 3.040 nonbonded pdb=" N TRP D 105 " pdb=" OE2 GLU R 340 " model vdw 2.325 3.120 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.340 3.040 nonbonded pdb=" O LEU L 34 " pdb=" N GLY L 51 " model vdw 2.342 3.120 ... (remaining 35712 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 35.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.170 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.009 0.481 4797 Z= 0.407 Angle : 0.819 24.611 6562 Z= 0.504 Chirality : 0.046 0.168 725 Planarity : 0.015 0.416 845 Dihedral : 13.305 78.592 1560 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 15.90 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.38 (0.34), residues: 627 helix: -4.58 (0.55), residues: 24 sheet: -1.33 (0.36), residues: 208 loop : -0.32 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.032 0.001 TYR B 37 PHE 0.014 0.001 PHE B 72 TRP 0.010 0.001 TRP B 36 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00866 / 0.37 ( 4788) covalent geometry : angle 0.78193 / 0.49 ( 6544) SS BOND : bond 0.08255 / 6.13 ( 9) SS BOND : angle 4.71299 / 2.88 ( 18) hydrogen bonds : bond 0.29628 / 18.78 ( 121) hydrogen bonds : angle 11.87417 / 8.23 ( 369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: H 50 TRP cc_start: 0.8203 (p-90) cc_final: 0.7905 (p-90) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0639 time to fit residues: 7.6484 Evaluate side-chains 80 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 116 ASN L 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130070 restraints weight = 6551.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133585 restraints weight = 3867.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135904 restraints weight = 2683.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137541 restraints weight = 2058.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138609 restraints weight = 1672.655| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4797 Z= 0.253 Angle : 0.624 9.250 6562 Z= 0.339 Chirality : 0.046 0.182 725 Planarity : 0.005 0.038 845 Dihedral : 4.568 15.187 698 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.07 % Allowed : 16.13 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.28 (0.35), residues: 627 helix: -3.80 (0.79), residues: 32 sheet: -1.33 (0.34), residues: 228 loop : -0.08 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 454 TYR 0.016 0.002 TYR R 453 PHE 0.013 0.002 PHE R 429 TRP 0.010 0.001 TRP H 113 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 ( 4788) covalent geometry : angle 0.62012 / 0.34 ( 6544) SS BOND : bond 0.00543 / 0.30 ( 9) SS BOND : angle 1.47703 / 0.89 ( 18) hydrogen bonds : bond 0.04727 / 2.99 ( 121) hydrogen bonds : angle 7.00543 / 4.82 ( 369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: H 50 TRP cc_start: 0.8128 (p-90) cc_final: 0.7770 (p-90) outliers start: 22 outliers final: 19 residues processed: 97 average time/residue: 0.0471 time to fit residues: 6.1383 Evaluate side-chains 95 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 448 ASN L 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126341 restraints weight = 6743.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129812 restraints weight = 3946.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132164 restraints weight = 2732.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133779 restraints weight = 2095.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134893 restraints weight = 1708.655| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4797 Z= 0.177 Angle : 0.554 6.562 6562 Z= 0.298 Chirality : 0.044 0.156 725 Planarity : 0.004 0.036 845 Dihedral : 4.389 15.648 698 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.61 % Allowed : 20.05 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.22 (0.35), residues: 627 helix: -3.55 (0.98), residues: 26 sheet: -1.25 (0.35), residues: 223 loop : -0.19 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 355 TYR 0.014 0.001 TYR R 369 PHE 0.010 0.001 PHE L 72 TRP 0.008 0.001 TRP H 113 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 4788) covalent geometry : angle 0.55066 / 0.30 ( 6544) SS BOND : bond 0.00507 / 0.29 ( 9) SS BOND : angle 1.32282 / 0.77 ( 18) hydrogen bonds : bond 0.03979 / 2.55 ( 121) hydrogen bonds : angle 6.28788 / 4.30 ( 369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: H 50 TRP cc_start: 0.8137 (p-90) cc_final: 0.7765 (p-90) outliers start: 20 outliers final: 18 residues processed: 98 average time/residue: 0.0446 time to fit residues: 5.8692 Evaluate side-chains 99 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130559 restraints weight = 6729.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134093 restraints weight = 3881.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136432 restraints weight = 2681.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138112 restraints weight = 2047.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139180 restraints weight = 1660.093| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4797 Z= 0.100 Angle : 0.494 6.836 6562 Z= 0.261 Chirality : 0.043 0.135 725 Planarity : 0.004 0.030 845 Dihedral : 3.982 15.465 698 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.61 % Allowed : 20.97 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -0.99 (0.35), residues: 627 helix: -3.05 (1.26), residues: 20 sheet: -1.08 (0.34), residues: 226 loop : -0.10 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 72 TYR 0.015 0.001 TYR R 369 PHE 0.009 0.001 PHE L 72 TRP 0.007 0.001 TRP R 436 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 4788) covalent geometry : angle 0.49113 / 0.26 ( 6544) SS BOND : bond 0.00391 / 0.22 ( 9) SS BOND : angle 1.07996 / 0.65 ( 18) hydrogen bonds : bond 0.03182 / 2.08 ( 121) hydrogen bonds : angle 5.66063 / 3.86 ( 369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: B 83 ASP cc_start: 0.8054 (t0) cc_final: 0.7850 (t0) REVERT: H 6 GLN cc_start: 0.8686 (mt0) cc_final: 0.8457 (mt0) REVERT: H 50 TRP cc_start: 0.8069 (p-90) cc_final: 0.7761 (p-90) REVERT: L 46 ARG cc_start: 0.7956 (ptm160) cc_final: 0.7378 (ptt-90) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 0.0481 time to fit residues: 6.3620 Evaluate side-chains 96 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 414 GLN Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125523 restraints weight = 6779.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129053 restraints weight = 3975.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131405 restraints weight = 2764.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132906 restraints weight = 2128.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134123 restraints weight = 1758.295| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4797 Z= 0.192 Angle : 0.541 6.132 6562 Z= 0.288 Chirality : 0.044 0.145 725 Planarity : 0.004 0.030 845 Dihedral : 4.305 16.128 698 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.30 % Allowed : 20.05 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.07 (0.34), residues: 627 helix: -3.05 (1.28), residues: 20 sheet: -1.15 (0.33), residues: 227 loop : -0.16 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 454 TYR 0.014 0.001 TYR R 453 PHE 0.013 0.001 PHE L 100 TRP 0.011 0.001 TRP D 47 HIS 0.001 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 4788) covalent geometry : angle 0.53767 / 0.29 ( 6544) SS BOND : bond 0.00467 / 0.26 ( 9) SS BOND : angle 1.22797 / 0.71 ( 18) hydrogen bonds : bond 0.03601 / 2.32 ( 121) hydrogen bonds : angle 5.80397 / 3.98 ( 369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8815 (mt0) cc_final: 0.8518 (mt0) outliers start: 23 outliers final: 23 residues processed: 100 average time/residue: 0.0453 time to fit residues: 6.0418 Evaluate side-chains 105 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 414 GLN Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128292 restraints weight = 6796.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131792 restraints weight = 3961.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134219 restraints weight = 2739.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135939 restraints weight = 2085.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137104 restraints weight = 1680.757| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4797 Z= 0.122 Angle : 0.497 6.425 6562 Z= 0.264 Chirality : 0.043 0.131 725 Planarity : 0.004 0.031 845 Dihedral : 4.040 15.811 698 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.30 % Allowed : 20.97 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.09 (0.34), residues: 627 helix: -3.59 (0.96), residues: 26 sheet: -0.97 (0.34), residues: 221 loop : -0.23 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 72 TYR 0.014 0.001 TYR R 369 PHE 0.009 0.001 PHE L 100 TRP 0.009 0.001 TRP R 436 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 4788) covalent geometry : angle 0.49481 / 0.26 ( 6544) SS BOND : bond 0.00380 / 0.21 ( 9) SS BOND : angle 1.05910 / 0.63 ( 18) hydrogen bonds : bond 0.03185 / 2.08 ( 121) hydrogen bonds : angle 5.48345 / 3.76 ( 369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8762 (mt0) cc_final: 0.8498 (mt0) REVERT: L 46 ARG cc_start: 0.7988 (ptm160) cc_final: 0.7393 (ptt-90) outliers start: 23 outliers final: 22 residues processed: 103 average time/residue: 0.0495 time to fit residues: 6.6325 Evaluate side-chains 105 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 414 GLN Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127735 restraints weight = 6726.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131195 restraints weight = 3900.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133390 restraints weight = 2697.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135128 restraints weight = 2089.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136219 restraints weight = 1692.049| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4797 Z= 0.137 Angle : 0.504 6.392 6562 Z= 0.269 Chirality : 0.043 0.136 725 Planarity : 0.004 0.029 845 Dihedral : 4.078 15.702 698 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.30 % Allowed : 20.74 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.03 (0.34), residues: 627 helix: -3.61 (0.96), residues: 26 sheet: -0.90 (0.34), residues: 221 loop : -0.21 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 454 TYR 0.013 0.001 TYR R 369 PHE 0.019 0.001 PHE L 100 TRP 0.009 0.001 TRP D 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4788) covalent geometry : angle 0.50171 / 0.27 ( 6544) SS BOND : bond 0.00379 / 0.21 ( 9) SS BOND : angle 1.07122 / 0.62 ( 18) hydrogen bonds : bond 0.03195 / 2.08 ( 121) hydrogen bonds : angle 5.45394 / 3.73 ( 369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8744 (mt0) cc_final: 0.8480 (mt0) REVERT: L 46 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7403 (ptt-90) outliers start: 23 outliers final: 21 residues processed: 100 average time/residue: 0.0526 time to fit residues: 6.9405 Evaluate side-chains 101 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 414 GLN Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 394 ASN L 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134229 restraints weight = 6472.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137644 restraints weight = 3869.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139912 restraints weight = 2681.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141548 restraints weight = 2050.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142638 restraints weight = 1651.254| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4797 Z= 0.156 Angle : 0.519 6.019 6562 Z= 0.278 Chirality : 0.044 0.138 725 Planarity : 0.004 0.028 845 Dihedral : 4.184 15.667 698 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.76 % Allowed : 21.66 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.02 (0.34), residues: 627 helix: -3.54 (1.00), residues: 26 sheet: -0.96 (0.34), residues: 223 loop : -0.16 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 454 TYR 0.013 0.001 TYR R 451 PHE 0.012 0.001 PHE L 100 TRP 0.010 0.001 TRP D 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4788) covalent geometry : angle 0.51604 / 0.28 ( 6544) SS BOND : bond 0.00383 / 0.21 ( 9) SS BOND : angle 1.12551 / 0.64 ( 18) hydrogen bonds : bond 0.03321 / 2.15 ( 121) hydrogen bonds : angle 5.45081 / 3.74 ( 369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8764 (mt0) cc_final: 0.8497 (mt0) REVERT: L 46 ARG cc_start: 0.7964 (ptm160) cc_final: 0.7377 (ptt-90) outliers start: 25 outliers final: 23 residues processed: 100 average time/residue: 0.0519 time to fit residues: 6.7490 Evaluate side-chains 103 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 414 GLN Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.151965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134310 restraints weight = 6366.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137597 restraints weight = 3809.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139919 restraints weight = 2667.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141420 restraints weight = 2024.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142580 restraints weight = 1650.688| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4797 Z= 0.157 Angle : 0.524 6.465 6562 Z= 0.281 Chirality : 0.044 0.138 725 Planarity : 0.004 0.029 845 Dihedral : 4.218 15.670 698 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.99 % Allowed : 21.43 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -1.03 (0.35), residues: 627 helix: -3.54 (1.00), residues: 26 sheet: -1.02 (0.34), residues: 228 loop : -0.10 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 24 TYR 0.017 0.001 TYR R 451 PHE 0.016 0.001 PHE L 100 TRP 0.009 0.001 TRP D 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 4788) covalent geometry : angle 0.52123 / 0.28 ( 6544) SS BOND : bond 0.00428 / 0.23 ( 9) SS BOND : angle 1.14437 / 0.64 ( 18) hydrogen bonds : bond 0.03326 / 2.14 ( 121) hydrogen bonds : angle 5.42260 / 3.72 ( 369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8753 (mt0) cc_final: 0.8505 (mt0) REVERT: L 46 ARG cc_start: 0.7966 (ptm160) cc_final: 0.7380 (ptt-90) outliers start: 26 outliers final: 23 residues processed: 102 average time/residue: 0.0526 time to fit residues: 6.9555 Evaluate side-chains 102 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 414 GLN Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135836 restraints weight = 6418.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139251 restraints weight = 3828.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141469 restraints weight = 2642.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143140 restraints weight = 2022.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144123 restraints weight = 1622.680| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4797 Z= 0.128 Angle : 0.515 6.995 6562 Z= 0.276 Chirality : 0.044 0.138 725 Planarity : 0.004 0.028 845 Dihedral : 4.097 15.574 698 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.61 % Allowed : 23.27 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -0.85 (0.35), residues: 627 helix: -3.08 (1.28), residues: 20 sheet: -0.93 (0.34), residues: 236 loop : -0.02 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.013 0.001 TYR R 369 PHE 0.032 0.001 PHE L 100 TRP 0.008 0.001 TRP D 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4788) covalent geometry : angle 0.51271 / 0.27 ( 6544) SS BOND : bond 0.00395 / 0.21 ( 9) SS BOND : angle 1.07161 / 0.62 ( 18) hydrogen bonds : bond 0.03198 / 2.06 ( 121) hydrogen bonds : angle 5.28479 / 3.63 ( 369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8741 (mt0) cc_final: 0.8468 (mt0) REVERT: L 46 ARG cc_start: 0.7954 (ptm160) cc_final: 0.7370 (ptt-90) outliers start: 20 outliers final: 20 residues processed: 97 average time/residue: 0.0460 time to fit residues: 5.8234 Evaluate side-chains 100 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 414 GLN Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 440 ASN Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 519 HIS Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134311 restraints weight = 6444.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137685 restraints weight = 3878.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139985 restraints weight = 2693.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141530 restraints weight = 2055.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142739 restraints weight = 1667.564| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4797 Z= 0.156 Angle : 0.534 6.774 6562 Z= 0.287 Chirality : 0.044 0.138 725 Planarity : 0.004 0.029 845 Dihedral : 4.218 15.599 698 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.07 % Allowed : 22.58 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: -0.88 (0.35), residues: 627 helix: -3.06 (1.29), residues: 20 sheet: -0.96 (0.34), residues: 228 loop : -0.06 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 24 TYR 0.013 0.001 TYR R 369 PHE 0.017 0.001 PHE L 100 TRP 0.009 0.001 TRP D 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 4788) covalent geometry : angle 0.53100 / 0.29 ( 6544) SS BOND : bond 0.00412 / 0.22 ( 9) SS BOND : angle 1.12932 / 0.64 ( 18) hydrogen bonds : bond 0.03365 / 2.17 ( 121) hydrogen bonds : angle 5.34837 / 3.68 ( 369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.82 seconds wall clock time: 23 minutes 19.12 seconds (1399.12 seconds total)