Starting phenix.real_space_refine on Wed Mar 5 15:33:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynt_33971/03_2025/7ynt_33971.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynt_33971/03_2025/7ynt_33971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ynt_33971/03_2025/7ynt_33971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynt_33971/03_2025/7ynt_33971.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynt_33971/03_2025/7ynt_33971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynt_33971/03_2025/7ynt_33971.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 1470 2.51 5 N 420 2.21 5 O 474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2364 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.44, per 1000 atoms: 0.61 Number of scatterers: 2364 At special positions: 0 Unit cell: (85.86, 107.06, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 474 8.00 N 420 7.00 C 1470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 320.3 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 44 through 55 removed outlier: 6.928A pdb=" N LYS F 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU A 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY F 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA F 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR A 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU B 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY A 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 58 through 66 removed outlier: 6.084A pdb=" N THR F 59 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN A 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU F 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N THR A 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL F 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN F 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR A 59 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 75 removed outlier: 6.857A pdb=" N VAL A 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL F 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR B 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.708A pdb=" N ALA F 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 94 through 95 removed outlier: 5.979A pdb=" N PHE F 94 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 89 removed outlier: 5.723A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 55 removed outlier: 6.953A pdb=" N LYS C 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU D 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY C 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA C 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR D 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS D 45 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU E 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY D 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL E 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL D 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 66 removed outlier: 6.068A pdb=" N THR C 59 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLN D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU C 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR D 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL D 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN C 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR D 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLN E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 69 through 75 removed outlier: 6.855A pdb=" N VAL D 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR D 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL E 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.720A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 89 removed outlier: 5.718A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 95 removed outlier: 5.981A pdb=" N PHE C 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 28 hydrogen bonds defined for protein. 84 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: 0.47 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 414 1.29 - 1.35: 378 1.35 - 1.42: 60 1.42 - 1.48: 396 1.48 - 1.54: 1122 Bond restraints: 2370 Sorted by residual: bond pdb=" C THR D 92 " pdb=" N GLY D 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 2.18e+00 bond pdb=" C THR A 92 " pdb=" N GLY A 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 2.16e+00 bond pdb=" C THR E 92 " pdb=" N GLY E 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.97e+00 bond pdb=" C THR C 92 " pdb=" N GLY C 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.88e+00 bond pdb=" C THR B 92 " pdb=" N GLY B 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.85e+00 ... (remaining 2365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 2969 1.04 - 2.07: 199 2.07 - 3.11: 24 3.11 - 4.14: 0 4.14 - 5.18: 6 Bond angle restraints: 3198 Sorted by residual: angle pdb=" N PHE A 94 " pdb=" CA PHE A 94 " pdb=" C PHE A 94 " ideal model delta sigma weight residual 108.24 103.06 5.18 1.81e+00 3.05e-01 8.19e+00 angle pdb=" N PHE E 94 " pdb=" CA PHE E 94 " pdb=" C PHE E 94 " ideal model delta sigma weight residual 108.24 103.08 5.16 1.81e+00 3.05e-01 8.12e+00 angle pdb=" N PHE B 94 " pdb=" CA PHE B 94 " pdb=" C PHE B 94 " ideal model delta sigma weight residual 108.24 103.08 5.16 1.81e+00 3.05e-01 8.12e+00 angle pdb=" N PHE D 94 " pdb=" CA PHE D 94 " pdb=" C PHE D 94 " ideal model delta sigma weight residual 108.24 103.09 5.15 1.81e+00 3.05e-01 8.09e+00 angle pdb=" N PHE F 94 " pdb=" CA PHE F 94 " pdb=" C PHE F 94 " ideal model delta sigma weight residual 108.24 103.10 5.14 1.81e+00 3.05e-01 8.06e+00 ... (remaining 3193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.95: 1028 7.95 - 15.90: 268 15.90 - 23.85: 54 23.85 - 31.80: 18 31.80 - 39.75: 24 Dihedral angle restraints: 1392 sinusoidal: 462 harmonic: 930 Sorted by residual: dihedral pdb=" CA ALA A 91 " pdb=" C ALA A 91 " pdb=" N THR A 92 " pdb=" CA THR A 92 " ideal model delta harmonic sigma weight residual -180.00 -166.25 -13.75 0 5.00e+00 4.00e-02 7.57e+00 dihedral pdb=" CA ALA D 91 " pdb=" C ALA D 91 " pdb=" N THR D 92 " pdb=" CA THR D 92 " ideal model delta harmonic sigma weight residual -180.00 -166.27 -13.73 0 5.00e+00 4.00e-02 7.54e+00 dihedral pdb=" CA ALA F 91 " pdb=" C ALA F 91 " pdb=" N THR F 92 " pdb=" CA THR F 92 " ideal model delta harmonic sigma weight residual 180.00 -166.27 -13.73 0 5.00e+00 4.00e-02 7.54e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.026: 171 0.026 - 0.052: 106 0.052 - 0.078: 72 0.078 - 0.103: 33 0.103 - 0.129: 44 Chirality restraints: 426 Sorted by residual: chirality pdb=" CA VAL F 71 " pdb=" N VAL F 71 " pdb=" C VAL F 71 " pdb=" CB VAL F 71 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 423 not shown) Planarity restraints: 396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 83 " -0.004 2.00e-02 2.50e+03 7.27e-03 5.28e-01 pdb=" C GLU E 83 " 0.013 2.00e-02 2.50e+03 pdb=" O GLU E 83 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY E 84 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 83 " 0.004 2.00e-02 2.50e+03 7.13e-03 5.09e-01 pdb=" C GLU F 83 " -0.012 2.00e-02 2.50e+03 pdb=" O GLU F 83 " 0.005 2.00e-02 2.50e+03 pdb=" N GLY F 84 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 83 " -0.004 2.00e-02 2.50e+03 7.10e-03 5.04e-01 pdb=" C GLU D 83 " 0.012 2.00e-02 2.50e+03 pdb=" O GLU D 83 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY D 84 " -0.004 2.00e-02 2.50e+03 ... (remaining 393 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 499 2.80 - 3.32: 2053 3.32 - 3.85: 3686 3.85 - 4.37: 3947 4.37 - 4.90: 7981 Nonbonded interactions: 18166 Sorted by model distance: nonbonded pdb=" NZ LYS E 60 " pdb=" OE1 GLN E 62 " model vdw 2.275 3.120 nonbonded pdb=" NZ LYS D 60 " pdb=" OE1 GLN D 62 " model vdw 2.275 3.120 nonbonded pdb=" NZ LYS C 60 " pdb=" OE1 GLN C 62 " model vdw 2.276 3.120 nonbonded pdb=" NZ LYS B 60 " pdb=" OE1 GLN B 62 " model vdw 2.276 3.120 nonbonded pdb=" NZ LYS A 60 " pdb=" OE1 GLN A 62 " model vdw 2.276 3.120 ... (remaining 18161 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.270 Find NCS groups from input model: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 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 : 0.004 0.019 2370 Z= 0.264 Angle : 0.590 5.180 3198 Z= 0.360 Chirality : 0.056 0.129 426 Planarity : 0.002 0.007 396 Dihedral : 11.350 39.754 804 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.55 (0.24), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.006 0.003 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1208 time to fit residues: 1.5108 Evaluate side-chains 3 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.222985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.195273 restraints weight = 3703.341| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 2.34 r_work: 0.4775 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4694 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2370 Z= 0.411 Angle : 0.638 5.395 3198 Z= 0.376 Chirality : 0.061 0.141 426 Planarity : 0.003 0.017 396 Dihedral : 5.823 14.338 342 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 3.33 % Allowed : 4.17 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.28), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.21), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS D 50 PHE 0.004 0.002 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 5 time to evaluate : 0.250 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 13 average time/residue: 0.0687 time to fit residues: 1.5749 Evaluate side-chains 8 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 3 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.209124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.182078 restraints weight = 3746.007| |-----------------------------------------------------------------------------| r_work (start): 0.4773 rms_B_bonded: 2.45 r_work: 0.4710 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.4630 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2370 Z= 0.364 Angle : 0.577 4.908 3198 Z= 0.338 Chirality : 0.059 0.136 426 Planarity : 0.003 0.015 396 Dihedral : 5.641 14.489 342 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.50 % Allowed : 6.25 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS D 50 PHE 0.007 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.203 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 16 average time/residue: 0.0591 time to fit residues: 1.5558 Evaluate side-chains 10 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN A 65 ASN C 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.210128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.183879 restraints weight = 3706.802| |-----------------------------------------------------------------------------| r_work (start): 0.4819 rms_B_bonded: 2.45 r_work: 0.4757 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.4676 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2370 Z= 0.212 Angle : 0.460 4.247 3198 Z= 0.273 Chirality : 0.055 0.129 426 Planarity : 0.002 0.010 396 Dihedral : 5.004 13.228 342 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.83 % Allowed : 10.42 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS D 50 PHE 0.009 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.251 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 12 average time/residue: 0.0806 time to fit residues: 1.6336 Evaluate side-chains 10 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN A 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.151283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.127437 restraints weight = 4455.171| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 3.51 r_work: 0.4497 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2370 Z= 0.422 Angle : 0.604 5.157 3198 Z= 0.362 Chirality : 0.060 0.144 426 Planarity : 0.003 0.011 396 Dihedral : 5.835 14.276 342 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.88 % Favored : 85.12 % Rotamer: Outliers : 3.33 % Allowed : 8.75 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS A 50 PHE 0.014 0.004 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.287 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 17 average time/residue: 0.0840 time to fit residues: 2.2511 Evaluate side-chains 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 8 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.152022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.128644 restraints weight = 4410.494| |-----------------------------------------------------------------------------| r_work (start): 0.4725 rms_B_bonded: 3.47 r_work: 0.4642 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 2370 Z= 0.313 Angle : 0.532 4.763 3198 Z= 0.317 Chirality : 0.057 0.134 426 Planarity : 0.002 0.010 396 Dihedral : 5.488 13.618 342 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS A 50 PHE 0.009 0.003 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.269 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 21 average time/residue: 0.0717 time to fit residues: 2.3432 Evaluate side-chains 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.0770 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.154468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.130411 restraints weight = 4477.981| |-----------------------------------------------------------------------------| r_work (start): 0.4820 rms_B_bonded: 3.50 r_work: 0.4729 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2370 Z= 0.235 Angle : 0.479 4.395 3198 Z= 0.286 Chirality : 0.055 0.132 426 Planarity : 0.002 0.010 396 Dihedral : 5.177 13.516 342 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.50 % Allowed : 11.67 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.40), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS D 50 PHE 0.008 0.003 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.264 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 17 average time/residue: 0.0743 time to fit residues: 2.0048 Evaluate side-chains 15 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.155536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.131156 restraints weight = 4413.330| |-----------------------------------------------------------------------------| r_work (start): 0.4828 rms_B_bonded: 3.48 r_work: 0.4736 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2370 Z= 0.225 Angle : 0.462 4.362 3198 Z= 0.277 Chirality : 0.055 0.131 426 Planarity : 0.002 0.010 396 Dihedral : 4.975 12.877 342 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.41), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS D 50 PHE 0.009 0.002 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.343 Fit side-chains REVERT: C 83 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6931 (tp30) outliers start: 5 outliers final: 5 residues processed: 18 average time/residue: 0.0929 time to fit residues: 2.5916 Evaluate side-chains 17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 12 optimal weight: 0.2980 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.153621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.129585 restraints weight = 4341.128| |-----------------------------------------------------------------------------| r_work (start): 0.4746 rms_B_bonded: 3.46 r_work: 0.4663 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2370 Z= 0.265 Angle : 0.491 4.491 3198 Z= 0.294 Chirality : 0.055 0.132 426 Planarity : 0.002 0.010 396 Dihedral : 5.138 13.111 342 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 2.50 % Allowed : 12.92 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.41), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS A 50 PHE 0.011 0.003 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.269 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 18 average time/residue: 0.0787 time to fit residues: 2.1982 Evaluate side-chains 17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN A 65 ASN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.151075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.127351 restraints weight = 4511.667| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 3.52 r_work: 0.4622 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2370 Z= 0.340 Angle : 0.545 4.800 3198 Z= 0.327 Chirality : 0.057 0.135 426 Planarity : 0.002 0.010 396 Dihedral : 5.460 13.527 342 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 2.50 % Allowed : 12.50 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.41), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS A 50 PHE 0.014 0.004 PHE D 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.271 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 17 average time/residue: 0.0698 time to fit residues: 1.9408 Evaluate side-chains 17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN A 65 ASN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.150512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.126630 restraints weight = 4453.719| |-----------------------------------------------------------------------------| r_work (start): 0.4717 rms_B_bonded: 3.53 r_work: 0.4628 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2370 Z= 0.350 Angle : 0.559 4.791 3198 Z= 0.335 Chirality : 0.058 0.137 426 Planarity : 0.003 0.010 396 Dihedral : 5.604 13.613 342 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Rotamer: Outliers : 2.50 % Allowed : 12.50 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.41), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS A 50 PHE 0.014 0.004 PHE D 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.43 seconds wall clock time: 24 minutes 38.47 seconds (1478.47 seconds total)