Starting phenix.real_space_refine on Fri Aug 22 14:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9k_36110/08_2025/8j9k_36110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9k_36110/08_2025/8j9k_36110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j9k_36110/08_2025/8j9k_36110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9k_36110/08_2025/8j9k_36110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j9k_36110/08_2025/8j9k_36110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9k_36110/08_2025/8j9k_36110.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2727 2.51 5 N 744 2.21 5 O 799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4284 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2542 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 12, 'TYR:plan': 2, 'ARG:plan': 9, 'GLU:plan': 14, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 785 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 957 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 1.51, per 1000 atoms: 0.35 Number of scatterers: 4284 At special positions: 0 Unit cell: (70.3779, 107.419, 106.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 799 8.00 N 744 7.00 C 2727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 112 " distance=2.04 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 122 " distance=2.03 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: 0.41 Conformation dependent library (CDL) restraints added in 210.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 6.4% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.965A pdb=" N LEU C 49 " --> pdb=" O PRO C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'D' and resid 88 through 91 Processing helix chain 'D' and resid 113 through 117 Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 118 removed outlier: 3.547A pdb=" N GLY C 40 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR C 7 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU C 391 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL C 9 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.687A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 16.110A pdb=" N GLN C 173 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 20.660A pdb=" N CYS C 141 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 144 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 54 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLN C 86 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL C 56 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR C 84 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 58 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 82 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS C 60 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.687A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 16.110A pdb=" N GLN C 173 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 20.660A pdb=" N CYS C 141 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 141 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 131 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 289 " --> pdb=" O GLN C 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 187 through 190 removed outlier: 3.514A pdb=" N THR C 187 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 201 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 223 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 209 through 211 removed outlier: 6.365A pdb=" N TYR C 210 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR C 323 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 345 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N VAL C 321 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 209 through 211 removed outlier: 6.365A pdb=" N TYR C 210 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR C 323 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 345 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N VAL C 321 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 232 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 233 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 260 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.560A pdb=" N THR B 96 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.814A pdb=" N ALA B 108 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 57 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR B 73 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP B 59 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.814A pdb=" N ALA B 108 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.553A pdb=" N CYS D 48 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 105 " --> pdb=" O CYS D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 86 removed outlier: 6.837A pdb=" N TRP D 62 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 76 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 60 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR D 139 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 85 through 86 removed outlier: 6.837A pdb=" N TRP D 62 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 76 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 60 " --> pdb=" O SER D 76 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 405 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: 0.70 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1401 1.34 - 1.46: 1030 1.46 - 1.58: 1931 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 4380 Sorted by residual: bond pdb=" C ASP C 136 " pdb=" N THR C 137 " ideal model delta sigma weight residual 1.331 1.277 0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" N GLN B 113 " pdb=" CA GLN B 113 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.67e+00 bond pdb=" C GLN C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.22e-02 6.72e+03 3.37e+00 bond pdb=" CA VAL C 316 " pdb=" CB VAL C 316 " ideal model delta sigma weight residual 1.542 1.521 0.021 1.33e-02 5.65e+03 2.49e+00 bond pdb=" CA VAL C 273 " pdb=" CB VAL C 273 " ideal model delta sigma weight residual 1.544 1.521 0.023 1.46e-02 4.69e+03 2.41e+00 ... (remaining 4375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 5793 1.84 - 3.68: 153 3.68 - 5.52: 25 5.52 - 7.36: 7 7.36 - 9.20: 3 Bond angle restraints: 5981 Sorted by residual: angle pdb=" CA GLN C 131 " pdb=" C GLN C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 119.06 112.37 6.69 1.05e+00 9.07e-01 4.06e+01 angle pdb=" O GLN C 131 " pdb=" C GLN C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 121.23 128.12 -6.89 1.13e+00 7.83e-01 3.72e+01 angle pdb=" C GLN C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 120.03 114.14 5.89 9.90e-01 1.02e+00 3.54e+01 angle pdb=" C SER B 74 " pdb=" N ALA B 75 " pdb=" CA ALA B 75 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" CA GLN B 113 " pdb=" C GLN B 113 " pdb=" O GLN B 113 " ideal model delta sigma weight residual 120.66 116.66 4.00 1.15e+00 7.56e-01 1.21e+01 ... (remaining 5976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 2342 17.71 - 35.42: 190 35.42 - 53.13: 54 53.13 - 70.84: 13 70.84 - 88.55: 5 Dihedral angle restraints: 2604 sinusoidal: 889 harmonic: 1715 Sorted by residual: dihedral pdb=" CB CYS B 47 " pdb=" SG CYS B 47 " pdb=" SG CYS B 112 " pdb=" CB CYS B 112 " ideal model delta sinusoidal sigma weight residual 93.00 35.49 57.51 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA TYR D 128 " pdb=" C TYR D 128 " pdb=" N TYR D 129 " pdb=" CA TYR D 129 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C GLN B 113 " pdb=" N GLN B 113 " pdb=" CA GLN B 113 " pdb=" CB GLN B 113 " ideal model delta harmonic sigma weight residual -122.60 -113.19 -9.41 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 2601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 547 0.051 - 0.101: 112 0.101 - 0.151: 35 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA GLN B 113 " pdb=" N GLN B 113 " pdb=" C GLN B 113 " pdb=" CB GLN B 113 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA VAL C 339 " pdb=" N VAL C 339 " pdb=" C VAL C 339 " pdb=" CB VAL C 339 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB VAL C 331 " pdb=" CA VAL C 331 " pdb=" CG1 VAL C 331 " pdb=" CG2 VAL C 331 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 693 not shown) Planarity restraints: 774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 132 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C TYR D 132 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR D 132 " -0.016 2.00e-02 2.50e+03 pdb=" N MET D 133 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 240 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR C 240 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR C 240 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 240 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 240 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 240 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 240 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 240 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 182 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO C 183 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " 0.022 5.00e-02 4.00e+02 ... (remaining 771 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 917 2.78 - 3.31: 4008 3.31 - 3.84: 6709 3.84 - 4.37: 7482 4.37 - 4.90: 13639 Nonbonded interactions: 32755 Sorted by model distance: nonbonded pdb=" NH2 ARG B 42 " pdb=" OG1 THR B 44 " model vdw 2.247 3.120 nonbonded pdb=" NH1 ARG D 64 " pdb=" OD1 ASP D 116 " model vdw 2.299 3.120 nonbonded pdb=" OE1 GLN D 108 " pdb=" ND2 ASN D 110 " model vdw 2.318 3.120 nonbonded pdb=" N GLU D 32 " pdb=" OE1 GLU D 32 " model vdw 2.318 3.120 nonbonded pdb=" O GLY C 133 " pdb=" N ASP C 136 " model vdw 2.359 3.120 ... (remaining 32750 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=1.00 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: 1.160 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.710 Find NCS groups from input model: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 0.055 4382 Z= 0.216 Angle : 0.767 9.204 5985 Z= 0.419 Chirality : 0.046 0.252 696 Planarity : 0.005 0.040 774 Dihedral : 15.318 88.546 1496 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.95 % Allowed : 19.05 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.34), residues: 582 helix: -3.14 (1.02), residues: 17 sheet: -1.19 (0.31), residues: 263 loop : -1.82 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 324 TYR 0.037 0.002 TYR C 240 PHE 0.012 0.002 PHE C 76 TRP 0.006 0.001 TRP D 73 HIS 0.003 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 4380) covalent geometry : angle 0.76280 ( 5981) SS BOND : bond 0.00711 ( 2) SS BOND : angle 3.02135 ( 4) hydrogen bonds : bond 0.23127 ( 139) hydrogen bonds : angle 10.46399 ( 405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.176 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 0.0677 time to fit residues: 6.2274 Evaluate side-chains 52 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 173 GLN D 108 GLN D 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.119757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094265 restraints weight = 9989.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097340 restraints weight = 5560.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099290 restraints weight = 3937.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100551 restraints weight = 3176.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.101350 restraints weight = 2744.355| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4382 Z= 0.163 Angle : 0.647 8.547 5985 Z= 0.327 Chirality : 0.044 0.160 696 Planarity : 0.005 0.039 774 Dihedral : 4.845 28.046 638 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.81 % Allowed : 18.33 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.33), residues: 582 helix: -3.12 (0.87), residues: 23 sheet: -0.96 (0.31), residues: 260 loop : -1.93 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.015 0.002 TYR C 240 PHE 0.011 0.001 PHE C 117 TRP 0.006 0.001 TRP D 62 HIS 0.002 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 4380) covalent geometry : angle 0.64524 ( 5981) SS BOND : bond 0.00673 ( 2) SS BOND : angle 1.87398 ( 4) hydrogen bonds : bond 0.03436 ( 139) hydrogen bonds : angle 6.38287 ( 405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: B 60 TYR cc_start: 0.8658 (m-10) cc_final: 0.8410 (m-10) REVERT: B 118 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6739 (m-30) outliers start: 16 outliers final: 7 residues processed: 75 average time/residue: 0.0615 time to fit residues: 6.2028 Evaluate side-chains 64 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS C 123 ASN B 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094930 restraints weight = 9997.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098039 restraints weight = 5601.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100031 restraints weight = 3969.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101264 restraints weight = 3192.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102192 restraints weight = 2763.980| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4382 Z= 0.131 Angle : 0.610 8.102 5985 Z= 0.306 Chirality : 0.043 0.155 696 Planarity : 0.004 0.039 774 Dihedral : 4.580 27.800 638 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.15 % Favored : 94.67 % Rotamer: Outliers : 3.10 % Allowed : 19.05 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.33), residues: 582 helix: -2.90 (0.95), residues: 23 sheet: -0.83 (0.31), residues: 264 loop : -1.75 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 100 TYR 0.012 0.001 TYR C 240 PHE 0.008 0.001 PHE C 116 TRP 0.005 0.001 TRP D 140 HIS 0.002 0.000 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4380) covalent geometry : angle 0.60860 ( 5981) SS BOND : bond 0.00525 ( 2) SS BOND : angle 1.46102 ( 4) hydrogen bonds : bond 0.02924 ( 139) hydrogen bonds : angle 5.55788 ( 405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8657 (m-40) cc_final: 0.8444 (m-40) REVERT: C 122 GLN cc_start: 0.7935 (pm20) cc_final: 0.7307 (pt0) REVERT: B 60 TYR cc_start: 0.8644 (m-10) cc_final: 0.8380 (m-10) REVERT: B 63 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8589 (mmmm) REVERT: B 118 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: D 128 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6508 (m-80) outliers start: 13 outliers final: 7 residues processed: 73 average time/residue: 0.0514 time to fit residues: 5.2744 Evaluate side-chains 68 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094687 restraints weight = 9869.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097756 restraints weight = 5557.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099777 restraints weight = 3958.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.101088 restraints weight = 3167.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.101856 restraints weight = 2736.826| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4382 Z= 0.146 Angle : 0.588 6.029 5985 Z= 0.298 Chirality : 0.043 0.152 696 Planarity : 0.005 0.076 774 Dihedral : 4.514 27.904 638 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.19 % Favored : 93.64 % Rotamer: Outliers : 3.81 % Allowed : 20.95 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.33), residues: 582 helix: -2.91 (0.94), residues: 23 sheet: -0.82 (0.31), residues: 272 loop : -1.75 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.013 0.001 TYR C 240 PHE 0.008 0.001 PHE C 117 TRP 0.004 0.001 TRP B 59 HIS 0.005 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4380) covalent geometry : angle 0.58725 ( 5981) SS BOND : bond 0.00580 ( 2) SS BOND : angle 1.47239 ( 4) hydrogen bonds : bond 0.02707 ( 139) hydrogen bonds : angle 5.28556 ( 405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.182 Fit side-chains REVERT: C 16 ASN cc_start: 0.8696 (m-40) cc_final: 0.8488 (m-40) REVERT: C 122 GLN cc_start: 0.7857 (pm20) cc_final: 0.7410 (pt0) REVERT: B 63 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8589 (mmmm) REVERT: B 118 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6710 (m-30) REVERT: D 128 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.6715 (m-80) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 0.0483 time to fit residues: 4.6543 Evaluate side-chains 68 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 15 optimal weight: 0.0170 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN C 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095620 restraints weight = 9839.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098700 restraints weight = 5495.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100731 restraints weight = 3900.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.101898 restraints weight = 3113.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.102863 restraints weight = 2706.804| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4382 Z= 0.124 Angle : 0.570 7.257 5985 Z= 0.286 Chirality : 0.043 0.168 696 Planarity : 0.005 0.067 774 Dihedral : 4.426 27.702 638 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 4.29 % Allowed : 20.95 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.33), residues: 582 helix: -2.87 (0.95), residues: 23 sheet: -0.73 (0.31), residues: 272 loop : -1.67 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 100 TYR 0.016 0.001 TYR C 240 PHE 0.008 0.001 PHE C 116 TRP 0.004 0.001 TRP D 140 HIS 0.005 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4380) covalent geometry : angle 0.56919 ( 5981) SS BOND : bond 0.00519 ( 2) SS BOND : angle 1.24005 ( 4) hydrogen bonds : bond 0.02570 ( 139) hydrogen bonds : angle 5.13052 ( 405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.184 Fit side-chains REVERT: C 16 ASN cc_start: 0.8699 (m-40) cc_final: 0.8498 (m-40) REVERT: C 103 ASP cc_start: 0.8380 (t70) cc_final: 0.7777 (t0) REVERT: C 122 GLN cc_start: 0.7903 (pm20) cc_final: 0.7380 (pt0) REVERT: C 240 TYR cc_start: 0.8356 (m-80) cc_final: 0.8100 (m-80) REVERT: B 118 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: D 128 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7001 (m-80) outliers start: 18 outliers final: 12 residues processed: 73 average time/residue: 0.0538 time to fit residues: 5.4128 Evaluate side-chains 69 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.120191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095497 restraints weight = 10034.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098659 restraints weight = 5419.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.100715 restraints weight = 3781.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.102004 restraints weight = 3012.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102493 restraints weight = 2589.963| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4382 Z= 0.137 Angle : 0.567 6.372 5985 Z= 0.286 Chirality : 0.043 0.158 696 Planarity : 0.004 0.054 774 Dihedral : 4.384 28.095 638 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.87 % Favored : 92.96 % Rotamer: Outliers : 4.29 % Allowed : 20.48 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.33), residues: 582 helix: -2.96 (0.81), residues: 29 sheet: -0.55 (0.32), residues: 261 loop : -1.65 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 170 TYR 0.016 0.001 TYR C 240 PHE 0.009 0.001 PHE C 116 TRP 0.004 0.001 TRP B 59 HIS 0.005 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4380) covalent geometry : angle 0.56574 ( 5981) SS BOND : bond 0.00559 ( 2) SS BOND : angle 1.33872 ( 4) hydrogen bonds : bond 0.02518 ( 139) hydrogen bonds : angle 5.06406 ( 405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.170 Fit side-chains REVERT: C 103 ASP cc_start: 0.8385 (t70) cc_final: 0.7676 (t0) REVERT: C 122 GLN cc_start: 0.7878 (pm20) cc_final: 0.7399 (pt0) REVERT: C 240 TYR cc_start: 0.8463 (m-80) cc_final: 0.8086 (m-80) REVERT: B 118 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: D 128 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7009 (m-80) outliers start: 18 outliers final: 13 residues processed: 70 average time/residue: 0.0471 time to fit residues: 4.7419 Evaluate side-chains 67 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.121929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.097251 restraints weight = 10079.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100362 restraints weight = 5568.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.102277 restraints weight = 3925.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103631 restraints weight = 3155.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104327 restraints weight = 2718.454| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4382 Z= 0.130 Angle : 0.557 5.858 5985 Z= 0.282 Chirality : 0.043 0.150 696 Planarity : 0.004 0.036 774 Dihedral : 4.323 27.854 638 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.67 % Favored : 94.16 % Rotamer: Outliers : 5.24 % Allowed : 20.48 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.34), residues: 582 helix: -2.87 (0.82), residues: 29 sheet: -0.46 (0.32), residues: 261 loop : -1.62 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 100 TYR 0.016 0.001 TYR C 240 PHE 0.008 0.001 PHE C 117 TRP 0.004 0.001 TRP B 59 HIS 0.006 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4380) covalent geometry : angle 0.55649 ( 5981) SS BOND : bond 0.00527 ( 2) SS BOND : angle 1.25264 ( 4) hydrogen bonds : bond 0.02481 ( 139) hydrogen bonds : angle 4.91955 ( 405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.180 Fit side-chains REVERT: C 103 ASP cc_start: 0.8365 (t70) cc_final: 0.7602 (t0) REVERT: C 122 GLN cc_start: 0.7852 (pm20) cc_final: 0.7381 (pt0) REVERT: C 240 TYR cc_start: 0.8545 (m-80) cc_final: 0.8134 (m-80) REVERT: B 63 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8609 (mmtm) REVERT: B 118 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6913 (m-30) REVERT: D 128 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7037 (m-80) outliers start: 22 outliers final: 14 residues processed: 74 average time/residue: 0.0491 time to fit residues: 5.0130 Evaluate side-chains 72 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 0.0000 chunk 15 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.120303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095712 restraints weight = 9846.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098821 restraints weight = 5344.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100777 restraints weight = 3768.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102091 restraints weight = 3022.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102799 restraints weight = 2613.674| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4382 Z= 0.137 Angle : 0.575 8.200 5985 Z= 0.286 Chirality : 0.043 0.144 696 Planarity : 0.004 0.036 774 Dihedral : 4.333 29.452 638 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 5.48 % Allowed : 20.71 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.34), residues: 582 helix: -2.69 (0.84), residues: 29 sheet: -0.36 (0.33), residues: 257 loop : -1.60 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 42 TYR 0.016 0.001 TYR C 240 PHE 0.009 0.001 PHE C 116 TRP 0.004 0.001 TRP B 59 HIS 0.003 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4380) covalent geometry : angle 0.57392 ( 5981) SS BOND : bond 0.00567 ( 2) SS BOND : angle 1.30115 ( 4) hydrogen bonds : bond 0.02501 ( 139) hydrogen bonds : angle 4.91098 ( 405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.177 Fit side-chains REVERT: C 103 ASP cc_start: 0.8353 (t70) cc_final: 0.7619 (t0) REVERT: C 122 GLN cc_start: 0.7842 (pm20) cc_final: 0.7378 (pt0) REVERT: C 240 TYR cc_start: 0.8554 (m-80) cc_final: 0.8077 (m-80) REVERT: C 289 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7861 (pp) REVERT: B 118 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: D 128 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.6589 (m-80) outliers start: 23 outliers final: 16 residues processed: 73 average time/residue: 0.0445 time to fit residues: 4.5522 Evaluate side-chains 73 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN C 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095601 restraints weight = 9893.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098678 restraints weight = 5366.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100777 restraints weight = 3779.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101997 restraints weight = 3024.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.102905 restraints weight = 2620.991| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4382 Z= 0.142 Angle : 0.578 7.510 5985 Z= 0.289 Chirality : 0.043 0.144 696 Planarity : 0.004 0.036 774 Dihedral : 4.322 29.050 638 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.19 % Favored : 93.64 % Rotamer: Outliers : 4.52 % Allowed : 21.67 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.34), residues: 582 helix: -2.57 (0.88), residues: 29 sheet: -0.32 (0.33), residues: 257 loop : -1.57 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 42 TYR 0.018 0.002 TYR C 210 PHE 0.009 0.001 PHE C 116 TRP 0.004 0.001 TRP D 73 HIS 0.003 0.000 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4380) covalent geometry : angle 0.57732 ( 5981) SS BOND : bond 0.00536 ( 2) SS BOND : angle 1.31226 ( 4) hydrogen bonds : bond 0.02557 ( 139) hydrogen bonds : angle 4.89270 ( 405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.139 Fit side-chains REVERT: C 103 ASP cc_start: 0.8399 (t70) cc_final: 0.7677 (t0) REVERT: C 122 GLN cc_start: 0.7836 (pm20) cc_final: 0.7373 (pt0) REVERT: C 240 TYR cc_start: 0.8551 (m-80) cc_final: 0.8038 (m-80) REVERT: C 289 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7862 (pp) REVERT: D 128 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6371 (m-80) outliers start: 19 outliers final: 15 residues processed: 68 average time/residue: 0.0397 time to fit residues: 3.8078 Evaluate side-chains 71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.0570 chunk 56 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097328 restraints weight = 9920.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100501 restraints weight = 5359.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.102534 restraints weight = 3771.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.103771 restraints weight = 3016.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104594 restraints weight = 2612.964| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4382 Z= 0.109 Angle : 0.560 7.932 5985 Z= 0.277 Chirality : 0.043 0.142 696 Planarity : 0.004 0.037 774 Dihedral : 4.163 28.946 638 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.33 % Rotamer: Outliers : 3.81 % Allowed : 22.14 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.34), residues: 582 helix: -2.30 (0.94), residues: 29 sheet: -0.17 (0.33), residues: 256 loop : -1.53 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.014 0.001 TYR B 73 PHE 0.008 0.001 PHE C 116 TRP 0.004 0.001 TRP D 140 HIS 0.003 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4380) covalent geometry : angle 0.55944 ( 5981) SS BOND : bond 0.00437 ( 2) SS BOND : angle 1.02124 ( 4) hydrogen bonds : bond 0.02373 ( 139) hydrogen bonds : angle 4.70721 ( 405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.107 Fit side-chains REVERT: C 103 ASP cc_start: 0.8322 (t70) cc_final: 0.7934 (t0) REVERT: C 122 GLN cc_start: 0.7778 (pm20) cc_final: 0.7310 (pt0) REVERT: C 240 TYR cc_start: 0.8572 (m-80) cc_final: 0.8076 (m-80) REVERT: D 128 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6075 (m-80) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.0436 time to fit residues: 4.8270 Evaluate side-chains 72 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 13 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN C 123 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.121626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096966 restraints weight = 9971.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100185 restraints weight = 5467.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102202 restraints weight = 3836.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103552 restraints weight = 3066.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104423 restraints weight = 2632.641| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4382 Z= 0.115 Angle : 0.588 8.197 5985 Z= 0.292 Chirality : 0.043 0.143 696 Planarity : 0.004 0.036 774 Dihedral : 4.138 28.160 638 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.33 % Rotamer: Outliers : 3.57 % Allowed : 23.33 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.35), residues: 582 helix: -2.38 (0.91), residues: 29 sheet: -0.27 (0.32), residues: 271 loop : -1.39 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 100 TYR 0.014 0.001 TYR B 73 PHE 0.008 0.001 PHE C 117 TRP 0.003 0.001 TRP B 59 HIS 0.003 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4380) covalent geometry : angle 0.58701 ( 5981) SS BOND : bond 0.00486 ( 2) SS BOND : angle 1.11629 ( 4) hydrogen bonds : bond 0.02398 ( 139) hydrogen bonds : angle 4.66171 ( 405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 973.29 seconds wall clock time: 17 minutes 23.74 seconds (1043.74 seconds total)