Starting phenix.real_space_refine on Thu Jul 2 00:43:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wla_66051/07_2026/9wla_66051.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wla_66051/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9wla_66051/07_2026/9wla_66051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wla_66051/07_2026/9wla_66051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wla_66051/07_2026/9wla_66051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wla_66051/07_2026/9wla_66051.map" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 1.13, per 1000 atoms: 0.24 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: 0.28 Conformation dependent library (CDL) restraints added in 134.0 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: 0.16 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: 0.62 Time building geometry restraints manager: 0.37 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 25.260 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- 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 : 0.177 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: 0.0674 time to fit residues: 8.0138 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 : 0.177 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.148611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129996 restraints weight = 6542.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133514 restraints weight = 3836.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135864 restraints weight = 2659.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137488 restraints weight = 2028.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138560 restraints weight = 1645.913| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 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 = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1655 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= 0.252 Angle : 0.623 9.036 6562 Z= 0.339 Chirality : 0.046 0.183 725 Planarity : 0.005 0.038 845 Dihedral : 4.608 15.000 698 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.07 % Allowed : 16.36 % Favored : 78.57 % 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 (0.80), residues: 32 sheet: -1.34 (0.34), residues: 223 loop : -0.10 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 454 TYR 0.016 0.002 TYR B 50 PHE 0.014 0.002 PHE L 72 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 0.00584 / 0.25 ( 4788) covalent geometry : angle 0.61903 / 0.34 ( 6544) SS BOND : bond 0.00542 / 0.29 ( 9) SS BOND : angle 1.49907 / 0.90 ( 18) hydrogen bonds : bond 0.04797 / 3.04 ( 121) hydrogen bonds : angle 6.95395 / 4.78 ( 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 : 0.219 Fit side-chains revert: symmetry clash REVERT: H 50 TRP cc_start: 0.8117 (p-90) cc_final: 0.7759 (p-90) outliers start: 22 outliers final: 18 residues processed: 97 average time/residue: 0.0713 time to fit residues: 9.0452 Evaluate side-chains 94 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.147104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128214 restraints weight = 6714.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131668 restraints weight = 3903.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134040 restraints weight = 2704.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135617 restraints weight = 2063.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136804 restraints weight = 1685.078| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4797 Z= 0.141 Angle : 0.532 6.337 6562 Z= 0.284 Chirality : 0.044 0.146 725 Planarity : 0.004 0.035 845 Dihedral : 4.248 15.901 698 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.92 % Allowed : 20.28 % Favored : 75.81 % 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: -1.18 (0.35), residues: 627 helix: -3.55 (0.98), residues: 26 sheet: -1.20 (0.34), residues: 222 loop : -0.18 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.015 0.001 TYR R 369 PHE 0.010 0.001 PHE L 72 TRP 0.007 0.001 TRP H 113 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 4788) covalent geometry : angle 0.52876 / 0.28 ( 6544) SS BOND : bond 0.00475 / 0.27 ( 9) SS BOND : angle 1.23983 / 0.73 ( 18) hydrogen bonds : bond 0.03781 / 2.43 ( 121) hydrogen bonds : angle 6.14982 / 4.20 ( 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 99 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: L 46 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7412 (ptt-90) outliers start: 17 outliers final: 16 residues processed: 94 average time/residue: 0.0685 time to fit residues: 8.4469 Evaluate side-chains 95 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain R residue 380 TYR 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 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: 0.8980 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.148035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129128 restraints weight = 6667.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132582 restraints weight = 3900.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134933 restraints weight = 2706.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136580 restraints weight = 2069.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137646 restraints weight = 1679.035| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- 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: 1 | |-----------------------------------------------------------------------------| |-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: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1970 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= 0.125 Angle : 0.508 6.688 6562 Z= 0.270 Chirality : 0.043 0.135 725 Planarity : 0.004 0.031 845 Dihedral : 4.074 14.822 698 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.30 % Allowed : 19.59 % Favored : 75.12 % 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: -1.09 (0.34), residues: 627 helix: -3.54 (0.97), residues: 26 sheet: -1.09 (0.34), residues: 226 loop : -0.13 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 72 TYR 0.014 0.001 TYR R 369 PHE 0.008 0.001 PHE L 72 TRP 0.008 0.001 TRP D 47 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4788) covalent geometry : angle 0.50470 / 0.27 ( 6544) SS BOND : bond 0.00429 / 0.24 ( 9) SS BOND : angle 1.14949 / 0.68 ( 18) hydrogen bonds : bond 0.03321 / 2.15 ( 121) hydrogen bonds : angle 5.73003 / 3.90 ( 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 107 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8716 (mt0) cc_final: 0.8479 (mt0) REVERT: L 46 ARG cc_start: 0.7965 (ptm160) cc_final: 0.7389 (ptt-90) outliers start: 23 outliers final: 20 residues processed: 101 average time/residue: 0.0697 time to fit residues: 9.2556 Evaluate side-chains 101 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 4 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 51 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.147521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128418 restraints weight = 6753.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131931 restraints weight = 3930.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134358 restraints weight = 2713.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136023 restraints weight = 2063.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137254 restraints weight = 1669.953| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4797 Z= 0.128 Angle : 0.503 6.457 6562 Z= 0.268 Chirality : 0.043 0.133 725 Planarity : 0.004 0.031 845 Dihedral : 4.039 15.464 698 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.84 % Allowed : 21.20 % 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: -0.95 (0.34), residues: 627 helix: -2.98 (1.29), residues: 20 sheet: -1.01 (0.34), residues: 226 loop : -0.12 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 454 TYR 0.014 0.001 TYR R 369 PHE 0.008 0.001 PHE L 72 TRP 0.008 0.001 TRP D 47 HIS 0.001 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4788) covalent geometry : angle 0.50050 / 0.27 ( 6544) SS BOND : bond 0.00412 / 0.23 ( 9) SS BOND : angle 1.09647 / 0.64 ( 18) hydrogen bonds : bond 0.03227 / 2.10 ( 121) hydrogen bonds : angle 5.59754 / 3.82 ( 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 101 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8735 (mt0) cc_final: 0.8483 (mt0) REVERT: L 46 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7389 (ptt-90) outliers start: 21 outliers final: 20 residues processed: 97 average time/residue: 0.0450 time to fit residues: 5.7036 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 : 0.128 ------------------------------------------------------------------------------- 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 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 4 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.146741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127603 restraints weight = 6789.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131110 restraints weight = 3960.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133516 restraints weight = 2730.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135083 restraints weight = 2079.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136309 restraints weight = 1700.798| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4797 Z= 0.139 Angle : 0.507 6.338 6562 Z= 0.271 Chirality : 0.044 0.135 725 Planarity : 0.004 0.029 845 Dihedral : 4.054 15.595 698 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.30 % Allowed : 20.28 % 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: -0.89 (0.35), residues: 627 helix: -2.97 (1.30), residues: 20 sheet: -0.94 (0.34), residues: 227 loop : -0.10 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 454 TYR 0.014 0.001 TYR R 369 PHE 0.012 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 0.00321 / 0.14 ( 4788) covalent geometry : angle 0.50413 / 0.27 ( 6544) SS BOND : bond 0.00404 / 0.23 ( 9) SS BOND : angle 1.11373 / 0.65 ( 18) hydrogen bonds : bond 0.03222 / 2.09 ( 121) hydrogen bonds : angle 5.50511 / 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 : 0.184 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8764 (mt0) cc_final: 0.8500 (mt0) REVERT: L 46 ARG cc_start: 0.7969 (ptm160) cc_final: 0.7405 (ptt-90) outliers start: 23 outliers final: 22 residues processed: 102 average time/residue: 0.0613 time to fit residues: 8.2525 Evaluate side-chains 104 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127271 restraints weight = 6729.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130746 restraints weight = 3930.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133175 restraints weight = 2730.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134762 restraints weight = 2077.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135958 restraints weight = 1696.538| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2182 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= 0.144 Angle : 0.511 6.292 6562 Z= 0.273 Chirality : 0.044 0.137 725 Planarity : 0.004 0.028 845 Dihedral : 4.080 15.607 698 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.76 % Allowed : 21.20 % Favored : 73.04 % 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: -0.86 (0.35), residues: 627 helix: -3.12 (1.24), residues: 20 sheet: -0.84 (0.35), residues: 221 loop : -0.14 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 454 TYR 0.013 0.001 TYR R 369 PHE 0.010 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 0.00334 / 0.14 ( 4788) covalent geometry : angle 0.50802 / 0.27 ( 6544) SS BOND : bond 0.00391 / 0.22 ( 9) SS BOND : angle 1.12149 / 0.64 ( 18) hydrogen bonds : bond 0.03232 / 2.10 ( 121) hydrogen bonds : angle 5.47768 / 3.75 ( 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 106 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8777 (mt0) cc_final: 0.8501 (mt0) REVERT: L 46 ARG cc_start: 0.7971 (ptm160) cc_final: 0.7383 (ptt-90) outliers start: 25 outliers final: 22 residues processed: 100 average time/residue: 0.0656 time to fit residues: 8.6157 Evaluate side-chains 101 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 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: 0.7980 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.146407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127120 restraints weight = 6817.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130641 restraints weight = 3966.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133099 restraints weight = 2747.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134740 restraints weight = 2092.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135957 restraints weight = 1701.955| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4797 Z= 0.148 Angle : 0.514 6.265 6562 Z= 0.276 Chirality : 0.044 0.137 725 Planarity : 0.004 0.029 845 Dihedral : 4.144 15.528 698 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.30 % Allowed : 21.43 % Favored : 73.27 % 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: -0.82 (0.35), residues: 627 helix: -3.16 (1.23), residues: 20 sheet: -0.81 (0.35), residues: 221 loop : -0.11 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 454 TYR 0.015 0.001 TYR R 451 PHE 0.009 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 0.00340 / 0.15 ( 4788) covalent geometry : angle 0.51142 / 0.27 ( 6544) SS BOND : bond 0.00381 / 0.21 ( 9) SS BOND : angle 1.15107 / 0.65 ( 18) hydrogen bonds : bond 0.03251 / 2.11 ( 121) hydrogen bonds : angle 5.44478 / 3.72 ( 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 102 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8772 (mt0) cc_final: 0.8495 (mt0) REVERT: L 46 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7389 (ptt-90) outliers start: 23 outliers final: 22 residues processed: 96 average time/residue: 0.0586 time to fit residues: 7.3315 Evaluate side-chains 101 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 0.0060 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.155511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138041 restraints weight = 6333.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141454 restraints weight = 3763.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143774 restraints weight = 2590.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145286 restraints weight = 1954.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146501 restraints weight = 1580.279| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4797 Z= 0.101 Angle : 0.490 6.573 6562 Z= 0.262 Chirality : 0.043 0.137 725 Planarity : 0.003 0.026 845 Dihedral : 3.877 15.246 698 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.38 % Allowed : 22.81 % Favored : 72.81 % 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: -0.73 (0.35), residues: 627 helix: -3.13 (1.25), residues: 20 sheet: -0.78 (0.35), residues: 226 loop : -0.01 (0.34), residues: 381 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 0.007 0.001 PHE L 72 TRP 0.009 0.001 TRP D 50 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 4788) covalent geometry : angle 0.48804 / 0.26 ( 6544) SS BOND : bond 0.00406 / 0.22 ( 9) SS BOND : angle 1.00489 / 0.58 ( 18) hydrogen bonds : bond 0.02983 / 1.95 ( 121) hydrogen bonds : angle 5.21829 / 3.56 ( 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 105 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8705 (mt0) cc_final: 0.8437 (mt0) REVERT: L 46 ARG cc_start: 0.7946 (ptm160) cc_final: 0.7365 (ptt-90) outliers start: 19 outliers final: 18 residues processed: 101 average time/residue: 0.0515 time to fit residues: 6.7795 Evaluate side-chains 101 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 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 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 16 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.150102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132130 restraints weight = 6465.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135446 restraints weight = 3910.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137699 restraints weight = 2732.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139296 restraints weight = 2098.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140420 restraints weight = 1699.427| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4797 Z= 0.218 Angle : 0.573 8.961 6562 Z= 0.306 Chirality : 0.045 0.150 725 Planarity : 0.004 0.029 845 Dihedral : 4.395 15.612 698 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.61 % Allowed : 22.35 % Favored : 73.04 % 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: -0.87 (0.35), residues: 627 helix: -2.99 (1.34), 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 0.003 0.001 ARG R 454 TYR 0.014 0.002 TYR R 453 PHE 0.018 0.002 PHE L 100 TRP 0.012 0.001 TRP D 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 4788) covalent geometry : angle 0.57003 / 0.30 ( 6544) SS BOND : bond 0.00471 / 0.25 ( 9) SS BOND : angle 1.28293 / 0.71 ( 18) hydrogen bonds : bond 0.03633 / 2.34 ( 121) hydrogen bonds : angle 5.56837 / 3.83 ( 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 104 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: R 403 ARG cc_start: 0.8136 (ptt90) cc_final: 0.7868 (ptp90) outliers start: 20 outliers final: 17 residues processed: 100 average time/residue: 0.0510 time to fit residues: 6.8241 Evaluate side-chains 100 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 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 401 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 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: 0.8980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.152895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135263 restraints weight = 6423.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138612 restraints weight = 3803.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140920 restraints weight = 2644.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142519 restraints weight = 2004.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143635 restraints weight = 1613.773| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2497 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= 0.135 Angle : 0.527 8.096 6562 Z= 0.280 Chirality : 0.044 0.138 725 Planarity : 0.004 0.028 845 Dihedral : 4.147 15.546 698 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.15 % Allowed : 24.19 % Favored : 71.66 % 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: -0.94 (0.35), residues: 627 helix: -3.55 (1.00), residues: 26 sheet: -0.89 (0.34), residues: 228 loop : -0.08 (0.34), residues: 373 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 0.015 0.001 PHE L 100 TRP 0.009 0.001 TRP D 47 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4788) covalent geometry : angle 0.52468 / 0.28 ( 6544) SS BOND : bond 0.00448 / 0.24 ( 9) SS BOND : angle 1.12870 / 0.63 ( 18) hydrogen bonds : bond 0.03219 / 2.09 ( 121) hydrogen bonds : angle 5.35185 / 3.68 ( 369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1400.80 seconds wall clock time: 24 minutes 49.91 seconds (1489.91 seconds total)