Starting phenix.real_space_refine on Tue Mar 3 19:47:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cr2_30445/03_2026/7cr2_30445_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cr2_30445/03_2026/7cr2_30445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2026/7cr2_30445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2026/7cr2_30445.map" model { file = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2026/7cr2_30445_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2026/7cr2_30445_trim.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 5500 2.51 5 N 1392 2.21 5 O 1344 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8276 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 1.41, per 1000 atoms: 0.17 Number of scatterers: 8276 At special positions: 0 Unit cell: (130.806, 130.806, 75.036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 F 4 9.00 O 1344 8.00 N 1392 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 233.1 milliseconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 85.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 91 through 113 removed outlier: 3.881A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.827A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.806A pdb=" N GLY A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 183 removed outlier: 3.699A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.510A pdb=" N HIS A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.644A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.657A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 113 removed outlier: 3.881A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.827A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.806A pdb=" N GLY B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.700A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.511A pdb=" N HIS B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.642A pdb=" N THR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 305 removed outlier: 3.657A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 91 through 113 removed outlier: 3.881A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 3.827A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 155 through 164 removed outlier: 3.806A pdb=" N GLY C 159 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 183 removed outlier: 3.700A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 210 Processing helix chain 'C' and resid 215 through 228 removed outlier: 3.511A pdb=" N HIS C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 254 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.642A pdb=" N THR C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 305 removed outlier: 3.657A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 330 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 91 through 113 removed outlier: 3.881A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.827A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.806A pdb=" N GLY D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 183 removed outlier: 3.700A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 215 through 228 removed outlier: 3.511A pdb=" N HIS D 228 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.642A pdb=" N THR D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 305 removed outlier: 3.657A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 330 628 hydrogen bonds defined for protein. 1884 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: 1.13 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1204 1.30 - 1.43: 2635 1.43 - 1.56: 4617 1.56 - 1.68: 0 1.68 - 1.81: 48 Bond restraints: 8504 Sorted by residual: bond pdb=" C17 FBX A 801 " pdb=" C19 FBX A 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C17 FBX D 801 " pdb=" C19 FBX D 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C17 FBX C 801 " pdb=" C19 FBX C 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C17 FBX B 801 " pdb=" C19 FBX B 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C13 FBX A 801 " pdb=" C14 FBX A 801 " ideal model delta sigma weight residual 1.385 1.510 -0.125 2.00e-02 2.50e+03 3.91e+01 ... (remaining 8499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 10842 1.78 - 3.56: 526 3.56 - 5.35: 108 5.35 - 7.13: 8 7.13 - 8.91: 24 Bond angle restraints: 11508 Sorted by residual: angle pdb=" CA TRP A 157 " pdb=" CB TRP A 157 " pdb=" CG TRP A 157 " ideal model delta sigma weight residual 113.60 118.68 -5.08 1.90e+00 2.77e-01 7.15e+00 angle pdb=" CA TRP B 157 " pdb=" CB TRP B 157 " pdb=" CG TRP B 157 " ideal model delta sigma weight residual 113.60 118.67 -5.07 1.90e+00 2.77e-01 7.11e+00 angle pdb=" CA TRP D 157 " pdb=" CB TRP D 157 " pdb=" CG TRP D 157 " ideal model delta sigma weight residual 113.60 118.67 -5.07 1.90e+00 2.77e-01 7.11e+00 angle pdb=" CA TRP C 157 " pdb=" CB TRP C 157 " pdb=" CG TRP C 157 " ideal model delta sigma weight residual 113.60 118.67 -5.07 1.90e+00 2.77e-01 7.11e+00 angle pdb=" N5 FBX D 801 " pdb=" C20 FBX D 801 " pdb=" O2 FBX D 801 " ideal model delta sigma weight residual 110.60 118.59 -7.99 3.00e+00 1.11e-01 7.09e+00 ... (remaining 11503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 4656 32.33 - 64.65: 132 64.65 - 96.98: 16 96.98 - 129.30: 0 129.30 - 161.63: 4 Dihedral angle restraints: 4808 sinusoidal: 1900 harmonic: 2908 Sorted by residual: dihedral pdb=" C8 FBX A 801 " pdb=" C7 FBX A 801 " pdb=" N4 FBX A 801 " pdb=" C9 FBX A 801 " ideal model delta sinusoidal sigma weight residual -75.46 86.17 -161.63 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C8 FBX C 801 " pdb=" C7 FBX C 801 " pdb=" N4 FBX C 801 " pdb=" C9 FBX C 801 " ideal model delta sinusoidal sigma weight residual -75.46 86.13 -161.59 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C8 FBX B 801 " pdb=" C7 FBX B 801 " pdb=" N4 FBX B 801 " pdb=" C9 FBX B 801 " ideal model delta sinusoidal sigma weight residual -75.46 86.13 -161.59 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 4805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 561 0.030 - 0.060: 452 0.060 - 0.091: 163 0.091 - 0.121: 67 0.121 - 0.151: 9 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA PRO B 308 " pdb=" N PRO B 308 " pdb=" C PRO B 308 " pdb=" CB PRO B 308 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA PRO D 308 " pdb=" N PRO D 308 " pdb=" C PRO D 308 " pdb=" CB PRO D 308 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA PRO C 308 " pdb=" N PRO C 308 " pdb=" C PRO C 308 " pdb=" CB PRO C 308 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1249 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 127 " -0.016 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR A 127 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 127 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 127 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 127 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 127 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 127 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 127 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 127 " 0.016 2.00e-02 2.50e+03 1.12e-02 2.49e+00 pdb=" CG TYR D 127 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 127 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 127 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 127 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 127 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 127 " 0.016 2.00e-02 2.50e+03 1.12e-02 2.49e+00 pdb=" CG TYR C 127 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 127 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 127 " 0.002 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 108 2.62 - 3.19: 8506 3.19 - 3.76: 12605 3.76 - 4.33: 17723 4.33 - 4.90: 27825 Nonbonded interactions: 66767 Sorted by model distance: nonbonded pdb=" O LEU C 107 " pdb=" OG SER C 110 " model vdw 2.052 3.040 nonbonded pdb=" O LEU B 107 " pdb=" OG SER B 110 " model vdw 2.052 3.040 nonbonded pdb=" O LEU D 107 " pdb=" OG SER D 110 " model vdw 2.052 3.040 nonbonded pdb=" O LEU A 107 " pdb=" OG SER A 110 " model vdw 2.053 3.040 nonbonded pdb=" O LEU C 176 " pdb=" OG SER C 179 " model vdw 2.255 3.040 ... (remaining 66762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.690 Find NCS groups from input model: 0.070 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.014 0.138 8504 Z= 0.640 Angle : 0.977 8.909 11508 Z= 0.510 Chirality : 0.048 0.151 1252 Planarity : 0.004 0.020 1392 Dihedral : 16.204 161.628 2952 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.48 % Allowed : 9.17 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.23), residues: 988 helix: -1.64 (0.15), residues: 776 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 201 TYR 0.027 0.003 TYR A 127 PHE 0.022 0.003 PHE A 297 TRP 0.025 0.002 TRP C 157 HIS 0.004 0.002 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.01378 ( 8504) covalent geometry : angle 0.97738 (11508) hydrogen bonds : bond 0.15274 ( 628) hydrogen bonds : angle 7.34977 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.328 Fit side-chains REVERT: A 174 MET cc_start: 0.1887 (ttp) cc_final: 0.1496 (tmm) REVERT: B 174 MET cc_start: 0.1883 (ttp) cc_final: 0.1502 (tmm) REVERT: C 174 MET cc_start: 0.1872 (ttp) cc_final: 0.1495 (tmm) REVERT: D 174 MET cc_start: 0.1874 (ttp) cc_final: 0.1496 (tmm) outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 0.1611 time to fit residues: 28.9410 Evaluate side-chains 119 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 228 HIS A 321 GLN B 78 GLN B 228 HIS B 321 GLN C 78 GLN C 228 HIS C 321 GLN D 78 GLN D 228 HIS D 321 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.196854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132312 restraints weight = 10856.780| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.42 r_work: 0.3337 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8504 Z= 0.180 Angle : 0.589 5.886 11508 Z= 0.314 Chirality : 0.040 0.129 1252 Planarity : 0.004 0.038 1392 Dihedral : 11.147 159.031 1140 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.26 % Allowed : 16.55 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 988 helix: 0.41 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -2.47 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 207 TYR 0.023 0.002 TYR A 82 PHE 0.014 0.002 PHE B 316 TRP 0.016 0.001 TRP A 157 HIS 0.002 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8504) covalent geometry : angle 0.58936 (11508) hydrogen bonds : bond 0.05953 ( 628) hydrogen bonds : angle 4.36519 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.309 Fit side-chains REVERT: B 321 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: C 321 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: D 321 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7585 (tt0) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.1275 time to fit residues: 25.1823 Evaluate side-chains 140 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 321 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 88 optimal weight: 0.0000 chunk 31 optimal weight: 0.3980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 83 ASN C 83 ASN D 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.201182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134261 restraints weight = 10779.643| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.98 r_work: 0.3419 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8504 Z= 0.127 Angle : 0.521 6.025 11508 Z= 0.274 Chirality : 0.036 0.112 1252 Planarity : 0.003 0.035 1392 Dihedral : 10.936 158.548 1140 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.10 % Allowed : 17.26 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 988 helix: 1.48 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -3.22 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 207 TYR 0.016 0.002 TYR D 141 PHE 0.017 0.002 PHE B 316 TRP 0.011 0.001 TRP A 157 HIS 0.001 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8504) covalent geometry : angle 0.52112 (11508) hydrogen bonds : bond 0.04803 ( 628) hydrogen bonds : angle 3.75796 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.6812 (tp30) cc_final: 0.6575 (tp30) REVERT: B 86 GLU cc_start: 0.6730 (tp30) cc_final: 0.6527 (tp30) REVERT: B 327 LYS cc_start: 0.7286 (ttpp) cc_final: 0.6802 (mttt) REVERT: C 86 GLU cc_start: 0.6734 (tp30) cc_final: 0.6532 (tp30) REVERT: C 327 LYS cc_start: 0.7322 (ttpp) cc_final: 0.6821 (mttt) REVERT: D 86 GLU cc_start: 0.6742 (tp30) cc_final: 0.6541 (tp30) outliers start: 26 outliers final: 7 residues processed: 159 average time/residue: 0.1305 time to fit residues: 26.1226 Evaluate side-chains 130 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 204 GLN C 204 GLN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.202164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135086 restraints weight = 10833.273| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.95 r_work: 0.3429 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8504 Z= 0.121 Angle : 0.509 6.401 11508 Z= 0.268 Chirality : 0.037 0.124 1252 Planarity : 0.003 0.031 1392 Dihedral : 10.856 158.484 1140 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.79 % Allowed : 19.88 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.27), residues: 988 helix: 1.80 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.77 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.013 0.001 TYR B 141 PHE 0.014 0.001 PHE D 297 TRP 0.013 0.001 TRP A 157 HIS 0.001 0.000 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8504) covalent geometry : angle 0.50881 (11508) hydrogen bonds : bond 0.04294 ( 628) hydrogen bonds : angle 3.48013 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.289 Fit side-chains REVERT: A 162 LYS cc_start: 0.5595 (pttp) cc_final: 0.5384 (pttp) outliers start: 15 outliers final: 9 residues processed: 141 average time/residue: 0.1262 time to fit residues: 22.4759 Evaluate side-chains 126 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.198657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130694 restraints weight = 10813.247| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.01 r_work: 0.3390 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8504 Z= 0.141 Angle : 0.509 5.985 11508 Z= 0.270 Chirality : 0.038 0.119 1252 Planarity : 0.003 0.026 1392 Dihedral : 10.839 158.244 1140 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 18.10 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 988 helix: 1.98 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -3.03 (0.36), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.012 0.001 TYR B 74 PHE 0.016 0.001 PHE D 137 TRP 0.012 0.001 TRP B 157 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8504) covalent geometry : angle 0.50926 (11508) hydrogen bonds : bond 0.04621 ( 628) hydrogen bonds : angle 3.50144 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.279 Fit side-chains REVERT: A 162 LYS cc_start: 0.5514 (pttp) cc_final: 0.5250 (pttp) outliers start: 30 outliers final: 26 residues processed: 147 average time/residue: 0.1154 time to fit residues: 21.6932 Evaluate side-chains 143 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.197218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129781 restraints weight = 10655.124| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.94 r_work: 0.3360 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8504 Z= 0.173 Angle : 0.540 6.113 11508 Z= 0.288 Chirality : 0.039 0.135 1252 Planarity : 0.003 0.028 1392 Dihedral : 10.850 156.562 1140 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.76 % Allowed : 16.79 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 988 helix: 1.96 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -3.13 (0.34), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 207 TYR 0.025 0.002 TYR D 82 PHE 0.019 0.002 PHE B 137 TRP 0.012 0.001 TRP A 157 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8504) covalent geometry : angle 0.53976 (11508) hydrogen bonds : bond 0.04888 ( 628) hydrogen bonds : angle 3.60208 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.299 Fit side-chains REVERT: A 162 LYS cc_start: 0.5444 (pttp) cc_final: 0.5148 (pttp) REVERT: A 328 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.5333 (t-90) REVERT: C 328 HIS cc_start: 0.6370 (OUTLIER) cc_final: 0.5411 (t-90) REVERT: D 328 HIS cc_start: 0.6364 (OUTLIER) cc_final: 0.5396 (t-90) outliers start: 40 outliers final: 26 residues processed: 156 average time/residue: 0.1082 time to fit residues: 22.1385 Evaluate side-chains 148 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 328 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN D 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.195847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128574 restraints weight = 10772.777| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.95 r_work: 0.3350 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8504 Z= 0.188 Angle : 0.554 6.683 11508 Z= 0.293 Chirality : 0.039 0.131 1252 Planarity : 0.003 0.029 1392 Dihedral : 10.843 154.198 1140 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.83 % Allowed : 16.67 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.27), residues: 988 helix: 1.94 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -3.22 (0.35), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 160 TYR 0.018 0.002 TYR D 82 PHE 0.018 0.002 PHE B 137 TRP 0.014 0.001 TRP C 157 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8504) covalent geometry : angle 0.55359 (11508) hydrogen bonds : bond 0.05009 ( 628) hydrogen bonds : angle 3.67424 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 119 time to evaluate : 0.201 Fit side-chains REVERT: A 162 LYS cc_start: 0.5515 (pttp) cc_final: 0.5163 (pttp) REVERT: A 328 HIS cc_start: 0.6378 (OUTLIER) cc_final: 0.5329 (t-90) REVERT: B 328 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.5336 (t-90) REVERT: C 328 HIS cc_start: 0.6554 (OUTLIER) cc_final: 0.5395 (t-90) REVERT: D 328 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.5379 (t-90) outliers start: 49 outliers final: 31 residues processed: 153 average time/residue: 0.1116 time to fit residues: 22.3445 Evaluate side-chains 150 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 328 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.192881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128222 restraints weight = 10639.911| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.29 r_work: 0.3267 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8504 Z= 0.268 Angle : 0.644 7.150 11508 Z= 0.343 Chirality : 0.043 0.148 1252 Planarity : 0.004 0.032 1392 Dihedral : 10.911 151.018 1140 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.36 % Allowed : 17.02 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.27), residues: 988 helix: 1.64 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -3.25 (0.39), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 160 TYR 0.017 0.002 TYR B 82 PHE 0.021 0.002 PHE B 137 TRP 0.016 0.002 TRP A 157 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 8504) covalent geometry : angle 0.64411 (11508) hydrogen bonds : bond 0.05702 ( 628) hydrogen bonds : angle 3.88895 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.230 Fit side-chains REVERT: A 162 LYS cc_start: 0.5353 (pttp) cc_final: 0.5085 (pttp) REVERT: A 328 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.5310 (t-90) REVERT: B 328 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.5274 (t-90) REVERT: C 328 HIS cc_start: 0.6501 (OUTLIER) cc_final: 0.5365 (t-90) REVERT: D 328 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5411 (t-90) outliers start: 45 outliers final: 37 residues processed: 158 average time/residue: 0.1072 time to fit residues: 22.1383 Evaluate side-chains 155 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 328 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.198863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132422 restraints weight = 10631.437| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.92 r_work: 0.3391 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8504 Z= 0.127 Angle : 0.515 6.836 11508 Z= 0.270 Chirality : 0.037 0.115 1252 Planarity : 0.003 0.030 1392 Dihedral : 10.768 150.861 1140 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 18.21 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.28), residues: 988 helix: 2.04 (0.19), residues: 832 sheet: None (None), residues: 0 loop : -3.13 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.016 0.001 TYR B 82 PHE 0.011 0.001 PHE B 137 TRP 0.011 0.001 TRP A 146 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8504) covalent geometry : angle 0.51523 (11508) hydrogen bonds : bond 0.04418 ( 628) hydrogen bonds : angle 3.57380 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.344 Fit side-chains REVERT: A 162 LYS cc_start: 0.5368 (pttp) cc_final: 0.4969 (ptmm) REVERT: A 328 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.5387 (t-90) REVERT: B 328 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.5445 (t-90) REVERT: C 328 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.5477 (t-90) REVERT: D 328 HIS cc_start: 0.6648 (OUTLIER) cc_final: 0.5468 (t-90) outliers start: 30 outliers final: 22 residues processed: 143 average time/residue: 0.1226 time to fit residues: 22.1913 Evaluate side-chains 136 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 0.0170 chunk 65 optimal weight: 0.8980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.197190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130607 restraints weight = 10578.995| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.89 r_work: 0.3371 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8504 Z= 0.161 Angle : 0.567 7.210 11508 Z= 0.298 Chirality : 0.039 0.124 1252 Planarity : 0.003 0.030 1392 Dihedral : 10.781 151.108 1140 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.57 % Allowed : 19.40 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.28), residues: 988 helix: 2.00 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -3.14 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.017 0.002 TYR B 82 PHE 0.014 0.001 PHE C 137 TRP 0.011 0.001 TRP A 146 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8504) covalent geometry : angle 0.56708 (11508) hydrogen bonds : bond 0.04716 ( 628) hydrogen bonds : angle 3.58962 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.315 Fit side-chains REVERT: A 162 LYS cc_start: 0.5357 (pttp) cc_final: 0.4952 (ptmm) REVERT: A 328 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5396 (t-90) REVERT: B 328 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.5373 (t-90) REVERT: C 328 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.5462 (t-90) REVERT: D 328 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.5451 (t-90) outliers start: 30 outliers final: 26 residues processed: 140 average time/residue: 0.1184 time to fit residues: 21.4196 Evaluate side-chains 144 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.196820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129907 restraints weight = 10585.400| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.91 r_work: 0.3358 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8504 Z= 0.169 Angle : 0.583 9.049 11508 Z= 0.301 Chirality : 0.039 0.127 1252 Planarity : 0.003 0.031 1392 Dihedral : 10.802 151.364 1140 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.69 % Allowed : 19.05 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.28), residues: 988 helix: 1.96 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -3.10 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.016 0.002 TYR C 82 PHE 0.015 0.002 PHE C 137 TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8504) covalent geometry : angle 0.58266 (11508) hydrogen bonds : bond 0.04754 ( 628) hydrogen bonds : angle 3.64050 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.83 seconds wall clock time: 46 minutes 33.04 seconds (2793.04 seconds total)