Starting phenix.real_space_refine on Tue Sep 24 16:06:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/09_2024/7cr2_30445_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/09_2024/7cr2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/09_2024/7cr2_30445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/09_2024/7cr2_30445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/09_2024/7cr2_30445_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/09_2024/7cr2_30445_trim.cif" } resolution = 3.2 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= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, D Time building chain proxies: 4.04, per 1000 atoms: 0.49 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.73 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: 2.46 Time building geometry restraints manager: 2.60 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: 0.00 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: 0.820 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.480 Find NCS groups from input model: 0.310 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- 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= 0.917 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 : 39.29 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 (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: -2.81 (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 TRP 0.025 0.002 TRP C 157 HIS 0.004 0.002 HIS C 96 PHE 0.022 0.003 PHE A 297 TYR 0.027 0.003 TYR A 127 ARG 0.008 0.001 ARG B 201 *********************** 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 fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.1501 (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: 0.3332 time to fit residues: 60.1836 Evaluate side-chains 120 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 B 78 GLN B 228 HIS C 78 GLN C 228 HIS D 78 GLN D 228 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2339 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= 0.263 Angle : 0.595 5.616 11508 Z= 0.319 Chirality : 0.040 0.130 1252 Planarity : 0.004 0.034 1392 Dihedral : 11.139 158.895 1140 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.14 % Allowed : 16.31 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 988 helix: 0.46 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -2.45 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 157 HIS 0.002 0.001 HIS A 324 PHE 0.015 0.002 PHE B 316 TYR 0.024 0.002 TYR D 82 ARG 0.005 0.001 ARG A 207 *********************** 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 162 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.786 Fit side-chains REVERT: A 162 LYS cc_start: 0.5675 (ptmt) cc_final: 0.5457 (pttp) outliers start: 18 outliers final: 18 residues processed: 162 average time/residue: 0.2857 time to fit residues: 57.8532 Evaluate side-chains 135 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8504 Z= 0.216 Angle : 0.525 5.783 11508 Z= 0.281 Chirality : 0.038 0.119 1252 Planarity : 0.003 0.039 1392 Dihedral : 10.914 157.374 1140 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.57 % Allowed : 17.50 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 988 helix: 1.30 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -2.82 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 157 HIS 0.001 0.001 HIS D 96 PHE 0.017 0.002 PHE A 316 TYR 0.015 0.002 TYR B 141 ARG 0.005 0.000 ARG D 207 *********************** 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 154 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 0.871 Fit side-chains REVERT: B 86 GLU cc_start: 0.6917 (tp30) cc_final: 0.6678 (tp30) REVERT: C 86 GLU cc_start: 0.6918 (tp30) cc_final: 0.6679 (tp30) REVERT: D 86 GLU cc_start: 0.6922 (tp30) cc_final: 0.6684 (tp30) outliers start: 30 outliers final: 18 residues processed: 150 average time/residue: 0.2750 time to fit residues: 52.0955 Evaluate side-chains 136 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 136 VAL 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 136 VAL 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 136 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3491 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= 0.201 Angle : 0.522 6.405 11508 Z= 0.277 Chirality : 0.038 0.140 1252 Planarity : 0.003 0.033 1392 Dihedral : 10.862 156.663 1140 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.21 % Allowed : 18.93 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 988 helix: 1.73 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.98 (0.39), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 157 HIS 0.002 0.001 HIS A 324 PHE 0.017 0.002 PHE A 137 TYR 0.013 0.001 TYR B 74 ARG 0.005 0.001 ARG A 207 *********************** 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 159 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7056 (tp30) cc_final: 0.6759 (tp30) REVERT: B 162 LYS cc_start: 0.5560 (pttp) cc_final: 0.5304 (pttp) REVERT: C 162 LYS cc_start: 0.5554 (pttp) cc_final: 0.5299 (pttp) outliers start: 27 outliers final: 19 residues processed: 158 average time/residue: 0.2802 time to fit residues: 55.5838 Evaluate side-chains 139 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 152 CYS 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 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 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 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 87 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8504 Z= 0.173 Angle : 0.504 6.936 11508 Z= 0.263 Chirality : 0.037 0.113 1252 Planarity : 0.003 0.022 1392 Dihedral : 10.769 155.891 1140 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.52 % Allowed : 19.05 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.27), residues: 988 helix: 1.98 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.77 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.002 0.001 HIS A 324 PHE 0.013 0.001 PHE B 137 TYR 0.012 0.001 TYR A 74 ARG 0.004 0.000 ARG A 87 *********************** 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 170 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 0.930 Fit side-chains REVERT: A 87 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6837 (tpp80) REVERT: A 219 LYS cc_start: 0.8565 (mttt) cc_final: 0.8359 (mtpt) REVERT: A 328 HIS cc_start: 0.6154 (OUTLIER) cc_final: 0.5170 (t-90) REVERT: B 162 LYS cc_start: 0.5596 (pttp) cc_final: 0.5373 (pttp) REVERT: B 328 HIS cc_start: 0.6058 (OUTLIER) cc_final: 0.5096 (t-90) REVERT: C 162 LYS cc_start: 0.5593 (pttp) cc_final: 0.5372 (pttp) REVERT: C 328 HIS cc_start: 0.6070 (OUTLIER) cc_final: 0.5111 (t-90) REVERT: D 162 LYS cc_start: 0.5505 (pttp) cc_final: 0.5275 (pttp) REVERT: D 328 HIS cc_start: 0.6061 (OUTLIER) cc_final: 0.5100 (t-90) outliers start: 38 outliers final: 27 residues processed: 165 average time/residue: 0.2703 time to fit residues: 57.8000 Evaluate side-chains 153 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 VAL 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 101 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 136 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8504 Z= 0.226 Angle : 0.519 6.351 11508 Z= 0.275 Chirality : 0.038 0.159 1252 Planarity : 0.003 0.025 1392 Dihedral : 10.768 154.892 1140 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.12 % Allowed : 17.86 % 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 (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: 1.91 (0.27), residues: 988 helix: 1.96 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.70 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.002 0.001 HIS A 324 PHE 0.016 0.001 PHE B 137 TYR 0.013 0.001 TYR A 74 ARG 0.004 0.000 ARG B 207 *********************** 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 172 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 0.920 Fit side-chains REVERT: A 219 LYS cc_start: 0.8597 (mttt) cc_final: 0.8390 (mtpt) REVERT: A 328 HIS cc_start: 0.6143 (OUTLIER) cc_final: 0.5043 (t-90) REVERT: B 328 HIS cc_start: 0.6130 (OUTLIER) cc_final: 0.5042 (t-90) REVERT: C 328 HIS cc_start: 0.6141 (OUTLIER) cc_final: 0.5062 (t-90) REVERT: D 328 HIS cc_start: 0.6130 (OUTLIER) cc_final: 0.5049 (t-90) outliers start: 43 outliers final: 30 residues processed: 165 average time/residue: 0.2456 time to fit residues: 52.7019 Evaluate side-chains 160 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 173 ILE Chi-restraints excluded: chain A residue 176 LEU 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 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 176 LEU 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 101 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 136 VAL 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 176 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 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8504 Z= 0.157 Angle : 0.486 6.371 11508 Z= 0.255 Chirality : 0.036 0.146 1252 Planarity : 0.003 0.025 1392 Dihedral : 10.675 154.514 1140 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.74 % Allowed : 20.24 % 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 (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: 2.20 (0.28), residues: 988 helix: 2.16 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.66 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 157 HIS 0.002 0.001 HIS A 324 PHE 0.010 0.001 PHE D 240 TYR 0.011 0.001 TYR B 141 ARG 0.003 0.000 ARG C 207 *********************** 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 149 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.976 Fit side-chains REVERT: A 328 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5110 (t-90) REVERT: B 162 LYS cc_start: 0.5517 (pttp) cc_final: 0.5248 (pttp) REVERT: B 328 HIS cc_start: 0.6260 (OUTLIER) cc_final: 0.5026 (t-90) REVERT: C 162 LYS cc_start: 0.5511 (pttp) cc_final: 0.5244 (pttp) REVERT: C 328 HIS cc_start: 0.6241 (OUTLIER) cc_final: 0.5011 (t-90) REVERT: D 162 LYS cc_start: 0.5429 (pttp) cc_final: 0.5190 (pttp) REVERT: D 328 HIS cc_start: 0.6304 (OUTLIER) cc_final: 0.5084 (t-90) outliers start: 23 outliers final: 19 residues processed: 149 average time/residue: 0.2344 time to fit residues: 45.8633 Evaluate side-chains 142 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain B residue 102 LEU 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 102 LEU Chi-restraints excluded: chain C residue 176 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 176 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 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4297 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= 0.163 Angle : 0.491 6.718 11508 Z= 0.257 Chirality : 0.036 0.148 1252 Planarity : 0.003 0.024 1392 Dihedral : 10.637 154.430 1140 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.45 % Allowed : 20.00 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.28), residues: 988 helix: 2.24 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.73 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.001 0.000 HIS A 324 PHE 0.010 0.001 PHE B 240 TYR 0.017 0.001 TYR A 82 ARG 0.002 0.000 ARG B 207 *********************** 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 152 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 0.957 Fit side-chains REVERT: A 328 HIS cc_start: 0.6358 (OUTLIER) cc_final: 0.5131 (t-90) REVERT: B 328 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.5128 (t-90) REVERT: C 328 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.5089 (t-90) REVERT: D 328 HIS cc_start: 0.6310 (OUTLIER) cc_final: 0.5080 (t-90) outliers start: 29 outliers final: 20 residues processed: 152 average time/residue: 0.2419 time to fit residues: 47.7121 Evaluate side-chains 144 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 102 LEU 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 102 LEU Chi-restraints excluded: chain C residue 176 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 176 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 92 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.0030 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4474 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= 0.161 Angle : 0.509 6.812 11508 Z= 0.262 Chirality : 0.037 0.152 1252 Planarity : 0.003 0.024 1392 Dihedral : 10.617 154.414 1140 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.86 % Allowed : 21.19 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.27), residues: 988 helix: 2.29 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.88 (0.39), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 146 HIS 0.002 0.001 HIS D 324 PHE 0.011 0.001 PHE B 240 TYR 0.025 0.001 TYR A 82 ARG 0.002 0.000 ARG D 207 *********************** 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 138 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.893 Fit side-chains REVERT: A 162 LYS cc_start: 0.5338 (pttp) cc_final: 0.5126 (pttp) REVERT: A 328 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5039 (t-90) REVERT: B 162 LYS cc_start: 0.5472 (pttp) cc_final: 0.5223 (pttp) REVERT: B 328 HIS cc_start: 0.6397 (OUTLIER) cc_final: 0.5040 (t-90) REVERT: C 162 LYS cc_start: 0.5467 (pttp) cc_final: 0.5219 (pttp) REVERT: C 328 HIS cc_start: 0.6406 (OUTLIER) cc_final: 0.5045 (t-90) REVERT: D 162 LYS cc_start: 0.5348 (pttp) cc_final: 0.5122 (pttp) REVERT: D 328 HIS cc_start: 0.6397 (OUTLIER) cc_final: 0.5032 (t-90) outliers start: 24 outliers final: 20 residues processed: 138 average time/residue: 0.2603 time to fit residues: 46.2770 Evaluate side-chains 137 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 102 LEU 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 102 LEU Chi-restraints excluded: chain C residue 176 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 176 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 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8504 Z= 0.187 Angle : 0.528 7.074 11508 Z= 0.270 Chirality : 0.038 0.144 1252 Planarity : 0.003 0.025 1392 Dihedral : 10.626 154.289 1140 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.98 % Allowed : 21.19 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.27), residues: 988 helix: 2.27 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.97 (0.37), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 146 HIS 0.002 0.001 HIS A 324 PHE 0.011 0.001 PHE A 297 TYR 0.024 0.001 TYR A 82 ARG 0.003 0.000 ARG A 160 ********************** 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 139 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 0.891 Fit side-chains REVERT: A 328 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.5001 (t-90) REVERT: B 162 LYS cc_start: 0.5506 (pttp) cc_final: 0.5274 (pttp) REVERT: B 328 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.5004 (t-90) REVERT: C 328 HIS cc_start: 0.6380 (OUTLIER) cc_final: 0.5015 (t-90) REVERT: D 328 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.5006 (t-90) outliers start: 25 outliers final: 21 residues processed: 139 average time/residue: 0.2471 time to fit residues: 44.5028 Evaluate side-chains 136 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 102 LEU 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 102 LEU Chi-restraints excluded: chain C residue 176 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 176 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 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.202213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.133804 restraints weight = 10545.094| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.00 r_work: 0.3430 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8504 Z= 0.162 Angle : 0.571 13.322 11508 Z= 0.276 Chirality : 0.038 0.153 1252 Planarity : 0.003 0.025 1392 Dihedral : 10.582 154.306 1140 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.45 % Allowed : 21.67 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.27), residues: 988 helix: 2.30 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -3.02 (0.36), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 146 HIS 0.002 0.001 HIS A 324 PHE 0.011 0.001 PHE A 240 TYR 0.019 0.001 TYR A 82 ARG 0.004 0.000 ARG A 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2108.01 seconds wall clock time: 37 minutes 59.37 seconds (2279.37 seconds total)