Starting phenix.real_space_refine on Thu Mar 6 01:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9k_36110/03_2025/8j9k_36110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9k_36110/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9k_36110/03_2025/8j9k_36110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9k_36110/03_2025/8j9k_36110.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9k_36110/03_2025/8j9k_36110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9k_36110/03_2025/8j9k_36110.cif" } resolution = 3.5 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= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 9} 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: {'PHE:plan': 1, 'GLU: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: 6.20, per 1000 atoms: 1.45 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: 1.61 Conformation dependent library (CDL) restraints added in 526.2 milliseconds 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: 0.99 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: 1.41 Time building geometry restraints manager: 1.84 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: 76.990 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.980 ------------------------------------------------------------------------------- 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 4380 Z= 0.299 Angle : 0.763 9.204 5981 Z= 0.417 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 (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: -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 TRP 0.006 0.001 TRP D 73 HIS 0.003 0.001 HIS C 114 PHE 0.012 0.002 PHE C 76 TYR 0.037 0.002 TYR C 240 ARG 0.004 0.001 ARG C 324 *********************** 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 : 0.405 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 0.2049 time to fit residues: 19.0831 Evaluate side-chains 51 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.0020 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.120680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095450 restraints weight = 9809.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098481 restraints weight = 5492.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100367 restraints weight = 3902.334| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4380 Z= 0.228 Angle : 0.641 8.447 5981 Z= 0.321 Chirality : 0.045 0.156 696 Planarity : 0.005 0.038 774 Dihedral : 4.769 27.722 638 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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 (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: -2.23 (0.34), residues: 582 helix: -3.07 (0.88), residues: 23 sheet: -0.93 (0.31), residues: 259 loop : -1.83 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 62 HIS 0.002 0.001 HIS C 114 PHE 0.009 0.001 PHE B 95 TYR 0.012 0.002 TYR C 240 ARG 0.003 0.000 ARG D 64 *********************** 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 77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 TYR cc_start: 0.8632 (m-10) cc_final: 0.8418 (m-10) REVERT: B 118 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: D 95 THR cc_start: 0.8529 (p) cc_final: 0.8298 (p) REVERT: D 108 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7915 (tm-30) outliers start: 13 outliers final: 5 residues processed: 74 average time/residue: 0.1684 time to fit residues: 16.5070 Evaluate side-chains 64 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 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 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3752 r_free = 0.3752 target = 0.120159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094761 restraints weight = 9938.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097802 restraints weight = 5567.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099799 restraints weight = 3948.386| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4380 Z= 0.230 Angle : 0.610 7.828 5981 Z= 0.304 Chirality : 0.043 0.155 696 Planarity : 0.004 0.038 774 Dihedral : 4.592 28.003 638 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 4.29 % Allowed : 18.57 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % 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: -2.15 (0.33), residues: 582 helix: -2.98 (0.93), residues: 23 sheet: -0.83 (0.31), residues: 262 loop : -1.83 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 62 HIS 0.002 0.000 HIS C 114 PHE 0.008 0.001 PHE C 117 TYR 0.014 0.001 TYR C 240 ARG 0.006 0.000 ARG C 100 *********************** 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 81 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8666 (m-40) cc_final: 0.8451 (m-40) REVERT: C 122 GLN cc_start: 0.7960 (pm20) cc_final: 0.7315 (pt0) REVERT: B 63 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8598 (mmmm) REVERT: B 118 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: D 128 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.6546 (m-80) outliers start: 18 outliers final: 11 residues processed: 75 average time/residue: 0.1191 time to fit residues: 12.3716 Evaluate side-chains 70 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 123 ASN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 239 GLN ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN D 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.120727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095015 restraints weight = 9977.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098098 restraints weight = 5552.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100141 restraints weight = 3937.060| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.218 Angle : 0.593 6.049 5981 Z= 0.300 Chirality : 0.043 0.152 696 Planarity : 0.005 0.076 774 Dihedral : 4.497 28.233 638 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.67 % Favored : 94.16 % Rotamer: Outliers : 4.29 % Allowed : 20.24 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % 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: -2.04 (0.33), residues: 582 helix: -2.88 (0.96), residues: 23 sheet: -0.81 (0.31), residues: 272 loop : -1.72 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 140 HIS 0.003 0.001 HIS C 114 PHE 0.008 0.001 PHE C 116 TYR 0.014 0.001 TYR B 60 ARG 0.006 0.000 ARG C 100 *********************** 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 78 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8676 (m-40) cc_final: 0.8473 (m-40) REVERT: C 122 GLN cc_start: 0.7854 (pm20) cc_final: 0.7402 (pt0) REVERT: B 63 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8586 (mmmm) REVERT: B 118 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: D 108 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: D 128 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6475 (m-80) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 0.1198 time to fit residues: 11.8088 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 : 0.454 ------------------------------------------------------------------------------- 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 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 108 GLN 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 38 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN D 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.120559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095269 restraints weight = 10080.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098349 restraints weight = 5534.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100432 restraints weight = 3898.435| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.206 Angle : 0.572 5.978 5981 Z= 0.291 Chirality : 0.043 0.149 696 Planarity : 0.005 0.067 774 Dihedral : 4.436 27.864 638 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.50 % Rotamer: Outliers : 4.52 % Allowed : 20.71 % 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 (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: -1.94 (0.33), residues: 582 helix: -2.85 (0.96), residues: 23 sheet: -0.72 (0.31), residues: 272 loop : -1.67 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 59 HIS 0.005 0.001 HIS C 347 PHE 0.008 0.001 PHE C 116 TYR 0.021 0.001 TYR C 240 ARG 0.005 0.000 ARG C 100 *********************** 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 81 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8700 (m-40) cc_final: 0.8495 (m-40) REVERT: C 103 ASP cc_start: 0.8367 (t70) cc_final: 0.7771 (t0) REVERT: C 122 GLN cc_start: 0.7927 (pm20) cc_final: 0.7426 (pt0) REVERT: B 118 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6551 (m-30) REVERT: D 128 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.6726 (m-80) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 0.1177 time to fit residues: 12.2688 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 : 0.442 ------------------------------------------------------------------------------- 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 126 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.121414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096077 restraints weight = 9914.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099184 restraints weight = 5543.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101184 restraints weight = 3947.371| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.182 Angle : 0.562 7.012 5981 Z= 0.282 Chirality : 0.043 0.180 696 Planarity : 0.004 0.059 774 Dihedral : 4.316 27.711 638 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 4.52 % Allowed : 21.19 % 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 (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: -1.88 (0.33), residues: 582 helix: -2.93 (0.83), residues: 29 sheet: -0.60 (0.31), residues: 266 loop : -1.65 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 140 HIS 0.004 0.001 HIS C 347 PHE 0.008 0.001 PHE C 116 TYR 0.019 0.001 TYR C 240 ARG 0.004 0.000 ARG C 100 *********************** 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 77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8354 (t70) cc_final: 0.7652 (t0) REVERT: C 122 GLN cc_start: 0.7882 (pm20) cc_final: 0.7393 (pt0) REVERT: B 118 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: D 108 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: D 128 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6716 (m-80) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.1138 time to fit residues: 10.9155 Evaluate side-chains 70 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU 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 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 108 GLN 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 44 optimal weight: 0.2980 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN D 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095952 restraints weight = 9971.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099061 restraints weight = 5570.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101078 restraints weight = 3957.806| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.198 Angle : 0.567 6.812 5981 Z= 0.286 Chirality : 0.043 0.172 696 Planarity : 0.004 0.044 774 Dihedral : 4.298 27.698 638 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.67 % Favored : 94.16 % Rotamer: Outliers : 5.48 % Allowed : 20.95 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % 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: -1.74 (0.34), residues: 582 helix: -2.84 (0.83), residues: 29 sheet: -0.45 (0.31), residues: 267 loop : -1.64 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 59 HIS 0.004 0.001 HIS C 347 PHE 0.008 0.001 PHE C 116 TYR 0.018 0.001 TYR C 240 ARG 0.004 0.000 ARG C 100 *********************** 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 79 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8353 (t70) cc_final: 0.7642 (t0) REVERT: C 122 GLN cc_start: 0.7867 (pm20) cc_final: 0.7369 (pt0) REVERT: B 118 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: D 108 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: D 128 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6706 (m-80) outliers start: 23 outliers final: 15 residues processed: 73 average time/residue: 0.1112 time to fit residues: 11.3765 Evaluate side-chains 71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 108 GLN 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 5 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN D 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.121405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096842 restraints weight = 9839.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099852 restraints weight = 5453.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101789 restraints weight = 3891.998| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4380 Z= 0.258 Angle : 0.585 6.275 5981 Z= 0.296 Chirality : 0.043 0.167 696 Planarity : 0.004 0.035 774 Dihedral : 4.387 27.651 638 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.53 % Favored : 93.30 % Rotamer: Outliers : 4.76 % Allowed : 21.67 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % 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: -1.75 (0.34), residues: 582 helix: -2.79 (0.84), residues: 29 sheet: -0.44 (0.31), residues: 267 loop : -1.66 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS C 347 PHE 0.009 0.001 PHE C 117 TYR 0.019 0.002 TYR C 240 ARG 0.004 0.000 ARG C 100 *********************** 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 74 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8375 (t70) cc_final: 0.7664 (t0) REVERT: C 122 GLN cc_start: 0.7906 (pm20) cc_final: 0.7430 (pt0) REVERT: B 106 ASP cc_start: 0.6998 (m-30) cc_final: 0.6795 (m-30) REVERT: B 118 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: D 128 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6946 (m-80) outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.1231 time to fit residues: 11.5662 Evaluate side-chains 67 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094634 restraints weight = 9985.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097706 restraints weight = 5409.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099625 restraints weight = 3825.059| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4380 Z= 0.272 Angle : 0.613 7.793 5981 Z= 0.312 Chirality : 0.044 0.162 696 Planarity : 0.004 0.035 774 Dihedral : 4.485 27.597 638 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.53 % Favored : 93.30 % Rotamer: Outliers : 4.76 % Allowed : 22.38 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.73 (0.34), residues: 582 helix: -2.64 (0.86), residues: 29 sheet: -0.45 (0.32), residues: 269 loop : -1.65 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 59 HIS 0.005 0.001 HIS C 347 PHE 0.009 0.001 PHE C 117 TYR 0.021 0.002 TYR C 240 ARG 0.004 0.000 ARG C 100 *********************** 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 75 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8399 (t70) cc_final: 0.7634 (t0) REVERT: C 122 GLN cc_start: 0.7886 (pm20) cc_final: 0.7424 (pt0) REVERT: B 118 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: D 128 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6723 (m-80) outliers start: 20 outliers final: 15 residues processed: 69 average time/residue: 0.1189 time to fit residues: 11.3634 Evaluate side-chains 70 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 108 GLN 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 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.120170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095805 restraints weight = 9760.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098825 restraints weight = 5489.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.100755 restraints weight = 3924.414| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.220 Angle : 0.595 7.929 5981 Z= 0.301 Chirality : 0.043 0.160 696 Planarity : 0.004 0.036 774 Dihedral : 4.395 27.685 638 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.67 % Favored : 94.16 % Rotamer: Outliers : 3.81 % Allowed : 23.33 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.58 (0.34), residues: 582 helix: -2.53 (0.90), residues: 29 sheet: -0.27 (0.32), residues: 267 loop : -1.64 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 73 HIS 0.003 0.001 HIS C 114 PHE 0.008 0.001 PHE C 116 TYR 0.025 0.001 TYR C 240 ARG 0.003 0.000 ARG C 100 ********************** 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 67 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8325 (t70) cc_final: 0.7533 (t0) REVERT: C 122 GLN cc_start: 0.7840 (pm20) cc_final: 0.7390 (pt0) REVERT: C 210 TYR cc_start: 0.7600 (m-80) cc_final: 0.7302 (m-80) REVERT: B 118 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: D 128 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6744 (m-80) outliers start: 16 outliers final: 14 residues processed: 63 average time/residue: 0.1204 time to fit residues: 10.6366 Evaluate side-chains 66 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 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 = 0.3778 r_free = 0.3778 target = 0.120557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095963 restraints weight = 9832.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.099046 restraints weight = 5405.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101055 restraints weight = 3833.801| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.217 Angle : 0.583 6.737 5981 Z= 0.295 Chirality : 0.043 0.157 696 Planarity : 0.004 0.036 774 Dihedral : 4.357 29.137 638 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 4.05 % Allowed : 23.10 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.43 (0.35), residues: 582 helix: -2.35 (0.91), residues: 29 sheet: -0.08 (0.33), residues: 258 loop : -1.60 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 73 HIS 0.003 0.001 HIS C 114 PHE 0.009 0.001 PHE C 116 TYR 0.022 0.001 TYR C 240 ARG 0.004 0.000 ARG C 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.22 seconds wall clock time: 35 minutes 7.03 seconds (2107.03 seconds total)