Starting phenix.real_space_refine on Fri Aug 22 22:35:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cr9_16805/08_2025/8cr9_16805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cr9_16805/08_2025/8cr9_16805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cr9_16805/08_2025/8cr9_16805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cr9_16805/08_2025/8cr9_16805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cr9_16805/08_2025/8cr9_16805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cr9_16805/08_2025/8cr9_16805.map" } resolution = 4.2 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= 0.002 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 11 5.16 5 C 2730 2.51 5 N 736 2.21 5 O 872 1.98 5 H 4272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3300 Classifications: {'peptide': 222} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain: "B" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3290 Classifications: {'peptide': 217} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "C" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2031 Classifications: {'peptide': 132} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 124} Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 8621 At special positions: 0 Unit cell: (64.6, 82.45, 105.4, 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 11 16.00 O 872 8.00 N 736 7.00 C 2730 6.00 H 4272 1.00 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: 0.49 Conformation dependent library (CDL) restraints added in 380.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 10 sheets defined 21.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.918A pdb=" N VAL A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 49' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'C' and resid 130 through 130 No H-bonds generated for 'chain 'C' and resid 130 through 130' Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 184 through 189 removed outlier: 4.243A pdb=" N ASP C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.797A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 235 through 261 removed outlier: 3.587A pdb=" N ARG C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) Proline residue: C 250 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.717A pdb=" N LEU A 18 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 removed outlier: 4.841A pdb=" N ALA A 146 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 193 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY A 148 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 191 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU A 150 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 189 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 152 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 187 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.668A pdb=" N THR A 214 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 7 removed outlier: 5.210A pdb=" N ASP B 17 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA8, first strand: chain 'B' and resid 117 through 121 removed outlier: 4.296A pdb=" N SER B 134 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 177 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 179 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B 165 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 163 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AB1, first strand: chain 'C' and resid 162 through 163 149 hydrogen bonds defined for protein. 390 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: 1.25 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4263 1.11 - 1.29: 731 1.29 - 1.47: 1478 1.47 - 1.64: 2230 1.64 - 1.82: 13 Bond restraints: 8715 Sorted by residual: bond pdb=" N LEU C 261 " pdb=" H LEU C 261 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TYR A 94 " pdb=" HD1 TYR A 94 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD2 TYR A 95 " pdb=" HD2 TYR A 95 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 TYR B 176 " pdb=" HE1 TYR B 176 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 TYR A 94 " pdb=" HE1 TYR A 94 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 8710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 13177 2.60 - 5.21: 1945 5.21 - 7.81: 548 7.81 - 10.41: 50 10.41 - 13.02: 11 Bond angle restraints: 15731 Sorted by residual: angle pdb=" N VAL B 83 " pdb=" CA VAL B 83 " pdb=" C VAL B 83 " ideal model delta sigma weight residual 112.17 119.58 -7.41 9.50e-01 1.11e+00 6.08e+01 angle pdb=" C TRP A 47 " pdb=" N VAL A 48 " pdb=" CA VAL A 48 " ideal model delta sigma weight residual 120.60 129.62 -9.02 1.29e+00 6.01e-01 4.89e+01 angle pdb=" CA PHE B 101 " pdb=" CB PHE B 101 " pdb=" CG PHE B 101 " ideal model delta sigma weight residual 113.80 120.28 -6.48 1.00e+00 1.00e+00 4.20e+01 angle pdb=" N TYR B 94 " pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 108.60 116.67 -8.07 1.46e+00 4.69e-01 3.06e+01 angle pdb=" N VAL A 48 " pdb=" CA VAL A 48 " pdb=" C VAL A 48 " ideal model delta sigma weight residual 110.36 116.06 -5.70 1.05e+00 9.07e-01 2.95e+01 ... (remaining 15726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3766 17.70 - 35.41: 277 35.41 - 53.11: 90 53.11 - 70.81: 17 70.81 - 88.51: 8 Dihedral angle restraints: 4158 sinusoidal: 2253 harmonic: 1905 Sorted by residual: dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N SER A 111 " pdb=" CA SER A 111 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA CYS B 88 " pdb=" C CYS B 88 " pdb=" N GLN B 89 " pdb=" CA GLN B 89 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PHE B 142 " pdb=" C PHE B 142 " pdb=" N TYR B 143 " pdb=" CA TYR B 143 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 4155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 401 0.087 - 0.174: 234 0.174 - 0.262: 36 0.262 - 0.349: 7 0.349 - 0.436: 3 Chirality restraints: 681 Sorted by residual: chirality pdb=" CA HIS B 96 " pdb=" N HIS B 96 " pdb=" C HIS B 96 " pdb=" CB HIS B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA LYS B 50 " pdb=" N LYS B 50 " pdb=" C LYS B 50 " pdb=" CB LYS B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA LYS C 258 " pdb=" N LYS C 258 " pdb=" C LYS C 258 " pdb=" CB LYS C 258 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 678 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 90 " 0.203 2.00e-02 2.50e+03 7.80e-02 1.83e+02 pdb=" CG TYR B 90 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 90 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR B 90 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR B 90 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 90 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 90 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 90 " 0.113 2.00e-02 2.50e+03 pdb=" HD1 TYR B 90 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 90 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 90 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR B 90 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " 0.195 2.00e-02 2.50e+03 7.42e-02 1.65e+02 pdb=" CG TYR A 59 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " 0.104 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 32 " -0.139 2.00e-02 2.50e+03 6.39e-02 1.64e+02 pdb=" CG TRP B 32 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP B 32 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 32 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP B 32 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP B 32 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP B 32 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 32 " -0.055 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 32 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP B 32 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 TRP B 32 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 TRP B 32 " 0.089 2.00e-02 2.50e+03 pdb=" HE3 TRP B 32 " 0.048 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 32 " -0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 32 " 0.117 2.00e-02 2.50e+03 pdb=" HH2 TRP B 32 " -0.046 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 627 2.19 - 2.80: 15346 2.80 - 3.40: 23113 3.40 - 4.00: 29818 4.00 - 4.60: 43383 Nonbonded interactions: 112287 Sorted by model distance: nonbonded pdb=" H ILE B 29 " pdb=" H GLY B 30 " model vdw 1.593 2.100 nonbonded pdb=" HG SER B 185 " pdb=" OD2 ASP B 188 " model vdw 1.615 2.450 nonbonded pdb=" HG SER C 206 " pdb=" OD2 ASP C 209 " model vdw 1.629 2.450 nonbonded pdb=" HG SER B 31 " pdb=" OE1 GLU B 66 " model vdw 1.629 2.450 nonbonded pdb=" HG SER A 186 " pdb=" OE1 GLN B 163 " model vdw 1.654 2.450 ... (remaining 112282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.220 Find NCS groups from input model: 0.040 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 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 : 0.013 0.047 4443 Z= 0.815 Angle : 1.974 10.053 6039 Z= 1.288 Chirality : 0.103 0.436 681 Planarity : 0.016 0.116 779 Dihedral : 14.418 88.513 1608 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 1.42 % Allowed : 9.56 % Favored : 89.03 % Rotamer: Outliers : 2.87 % Allowed : 3.69 % Favored : 93.44 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: -2.67 (0.32), residues: 565 helix: -1.12 (0.47), residues: 91 sheet: -0.78 (0.46), residues: 119 loop : -2.44 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 61 TYR 0.182 0.034 TYR B 90 PHE 0.061 0.014 PHE B 212 TRP 0.097 0.026 TRP A 36 HIS 0.017 0.004 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.01318 ( 4443) covalent geometry : angle 1.97446 ( 6039) hydrogen bonds : bond 0.16000 ( 149) hydrogen bonds : angle 8.35167 ( 390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8297 (p) cc_final: 0.8089 (m) REVERT: A 163 TRP cc_start: 0.6230 (m100) cc_final: 0.5285 (m100) REVERT: B 71 PHE cc_start: 0.6120 (t80) cc_final: 0.5349 (t80) REVERT: B 118 VAL cc_start: 0.8393 (t) cc_final: 0.8183 (p) REVERT: B 120 ILE cc_start: 0.3867 (mt) cc_final: 0.3625 (mt) outliers start: 14 outliers final: 8 residues processed: 147 average time/residue: 0.1342 time to fit residues: 24.4480 Evaluate side-chains 108 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.236114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.211236 restraints weight = 15877.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.217690 restraints weight = 12856.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.219900 restraints weight = 8003.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.220982 restraints weight = 5522.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.221420 restraints weight = 5264.217| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4443 Z= 0.174 Angle : 0.782 6.551 6039 Z= 0.422 Chirality : 0.046 0.177 681 Planarity : 0.006 0.046 779 Dihedral : 8.646 40.444 611 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.56 % Favored : 89.73 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.34), residues: 565 helix: -0.11 (0.53), residues: 98 sheet: -1.27 (0.42), residues: 147 loop : -2.28 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 44 TYR 0.027 0.003 TYR B 90 PHE 0.016 0.002 PHE B 142 TRP 0.014 0.001 TRP A 105 HIS 0.007 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4443) covalent geometry : angle 0.78185 ( 6039) hydrogen bonds : bond 0.05046 ( 149) hydrogen bonds : angle 7.09961 ( 390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7196 (m-30) cc_final: 0.6957 (m-30) REVERT: B 71 PHE cc_start: 0.4856 (t80) cc_final: 0.4425 (t80) REVERT: B 200 THR cc_start: 0.8316 (m) cc_final: 0.8078 (p) REVERT: C 220 GLU cc_start: 0.6457 (tp30) cc_final: 0.6040 (pm20) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1457 time to fit residues: 21.6054 Evaluate side-chains 96 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.220994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.190799 restraints weight = 15190.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.192893 restraints weight = 11836.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.195705 restraints weight = 10310.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.198366 restraints weight = 7531.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.200241 restraints weight = 6479.554| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4443 Z= 0.170 Angle : 0.707 6.144 6039 Z= 0.383 Chirality : 0.045 0.154 681 Planarity : 0.006 0.046 779 Dihedral : 7.806 37.691 611 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.21 % Favored : 87.26 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.33), residues: 565 helix: 0.07 (0.53), residues: 99 sheet: -1.39 (0.41), residues: 151 loop : -2.65 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 44 TYR 0.029 0.003 TYR B 90 PHE 0.014 0.002 PHE B 142 TRP 0.016 0.002 TRP C 186 HIS 0.008 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4443) covalent geometry : angle 0.70690 ( 6039) hydrogen bonds : bond 0.04596 ( 149) hydrogen bonds : angle 6.73470 ( 390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ASP cc_start: 0.7920 (t0) cc_final: 0.7295 (m-30) REVERT: B 200 THR cc_start: 0.8607 (m) cc_final: 0.8257 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1481 time to fit residues: 18.8003 Evaluate side-chains 88 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.222541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.197157 restraints weight = 15097.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.200425 restraints weight = 12623.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203099 restraints weight = 10029.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.203538 restraints weight = 6449.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.204809 restraints weight = 5650.569| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4443 Z= 0.167 Angle : 0.677 6.652 6039 Z= 0.365 Chirality : 0.043 0.139 681 Planarity : 0.006 0.061 779 Dihedral : 7.462 36.687 611 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.21 % Favored : 87.43 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.33), residues: 565 helix: 0.21 (0.53), residues: 99 sheet: -1.47 (0.39), residues: 156 loop : -2.74 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.027 0.002 TYR B 90 PHE 0.049 0.002 PHE B 142 TRP 0.009 0.001 TRP A 105 HIS 0.005 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4443) covalent geometry : angle 0.67685 ( 6039) hydrogen bonds : bond 0.04187 ( 149) hydrogen bonds : angle 6.65832 ( 390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7625 (mt0) cc_final: 0.7004 (mt0) REVERT: B 33 LEU cc_start: 0.7079 (pp) cc_final: 0.6743 (pp) REVERT: B 108 ASP cc_start: 0.7740 (t0) cc_final: 0.7300 (m-30) REVERT: B 200 THR cc_start: 0.8575 (m) cc_final: 0.8176 (p) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1678 time to fit residues: 20.7916 Evaluate side-chains 91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.217982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.192640 restraints weight = 15187.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195195 restraints weight = 12515.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.197842 restraints weight = 10151.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.198675 restraints weight = 6401.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.199498 restraints weight = 5718.609| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4443 Z= 0.202 Angle : 0.699 6.296 6039 Z= 0.377 Chirality : 0.045 0.140 681 Planarity : 0.006 0.051 779 Dihedral : 7.532 35.692 611 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.69 % Favored : 84.78 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.32), residues: 565 helix: 0.19 (0.52), residues: 99 sheet: -1.58 (0.41), residues: 144 loop : -3.15 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.031 0.003 TYR B 90 PHE 0.025 0.002 PHE B 142 TRP 0.017 0.002 TRP B 151 HIS 0.004 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4443) covalent geometry : angle 0.69896 ( 6039) hydrogen bonds : bond 0.04421 ( 149) hydrogen bonds : angle 6.56677 ( 390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7710 (mt0) cc_final: 0.7026 (mt0) REVERT: B 33 LEU cc_start: 0.7143 (pp) cc_final: 0.6790 (pp) REVERT: B 106 LYS cc_start: 0.7315 (mttt) cc_final: 0.6742 (mptt) REVERT: B 108 ASP cc_start: 0.7777 (t0) cc_final: 0.7254 (m-30) REVERT: B 170 ASP cc_start: 0.3928 (t70) cc_final: 0.3581 (t0) REVERT: B 200 THR cc_start: 0.8513 (m) cc_final: 0.8226 (p) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1533 time to fit residues: 17.4518 Evaluate side-chains 83 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.221191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.190929 restraints weight = 15011.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.193620 restraints weight = 11357.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.196650 restraints weight = 9008.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.199249 restraints weight = 6720.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.199636 restraints weight = 5648.372| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4443 Z= 0.145 Angle : 0.632 5.802 6039 Z= 0.338 Chirality : 0.043 0.138 681 Planarity : 0.006 0.054 779 Dihedral : 7.121 35.922 611 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.39 % Favored : 87.26 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.33), residues: 565 helix: 0.41 (0.54), residues: 99 sheet: -1.68 (0.39), residues: 157 loop : -3.01 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.028 0.002 TYR C 177 PHE 0.024 0.002 PHE B 142 TRP 0.013 0.002 TRP B 35 HIS 0.004 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4443) covalent geometry : angle 0.63217 ( 6039) hydrogen bonds : bond 0.03833 ( 149) hydrogen bonds : angle 6.35003 ( 390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7090 (pp) cc_final: 0.6735 (pp) REVERT: B 108 ASP cc_start: 0.7643 (t0) cc_final: 0.7149 (m-30) REVERT: B 148 LYS cc_start: 0.6921 (tppt) cc_final: 0.6684 (tppt) REVERT: B 200 THR cc_start: 0.8588 (m) cc_final: 0.8216 (p) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1731 time to fit residues: 18.5739 Evaluate side-chains 80 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.216770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.185737 restraints weight = 15580.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.189837 restraints weight = 11798.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.192278 restraints weight = 9388.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.195042 restraints weight = 7216.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.196270 restraints weight = 5946.480| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4443 Z= 0.214 Angle : 0.709 6.566 6039 Z= 0.379 Chirality : 0.045 0.138 681 Planarity : 0.006 0.056 779 Dihedral : 7.424 35.165 611 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.40 % Favored : 83.89 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.33), residues: 565 helix: 0.14 (0.52), residues: 99 sheet: -1.88 (0.38), residues: 157 loop : -3.28 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.030 0.003 TYR B 90 PHE 0.014 0.002 PHE B 142 TRP 0.015 0.002 TRP A 36 HIS 0.005 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 4443) covalent geometry : angle 0.70931 ( 6039) hydrogen bonds : bond 0.04297 ( 149) hydrogen bonds : angle 6.50209 ( 390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7203 (pp) cc_final: 0.6751 (pp) REVERT: B 106 LYS cc_start: 0.7453 (mttt) cc_final: 0.6874 (mptt) REVERT: B 108 ASP cc_start: 0.7573 (t0) cc_final: 0.7136 (m-30) REVERT: B 148 LYS cc_start: 0.6969 (tppt) cc_final: 0.6648 (tppt) REVERT: B 170 ASP cc_start: 0.4479 (t70) cc_final: 0.4261 (t0) REVERT: B 200 THR cc_start: 0.8604 (m) cc_final: 0.8219 (p) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1785 time to fit residues: 20.3906 Evaluate side-chains 80 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.218148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191753 restraints weight = 15159.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.192324 restraints weight = 13545.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.195785 restraints weight = 11717.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.196696 restraints weight = 8040.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.200654 restraints weight = 6900.334| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4443 Z= 0.166 Angle : 0.659 6.195 6039 Z= 0.350 Chirality : 0.044 0.132 681 Planarity : 0.006 0.053 779 Dihedral : 7.199 35.570 611 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.98 % Favored : 85.49 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.32), residues: 565 helix: 0.15 (0.52), residues: 99 sheet: -1.75 (0.39), residues: 151 loop : -3.27 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.025 0.002 TYR B 90 PHE 0.015 0.002 PHE B 142 TRP 0.014 0.002 TRP C 186 HIS 0.007 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4443) covalent geometry : angle 0.65866 ( 6039) hydrogen bonds : bond 0.03904 ( 149) hydrogen bonds : angle 6.42184 ( 390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.7150 (pp) cc_final: 0.6734 (pp) REVERT: B 106 LYS cc_start: 0.7376 (mttt) cc_final: 0.6748 (mptt) REVERT: B 108 ASP cc_start: 0.7649 (t0) cc_final: 0.7116 (m-30) REVERT: B 148 LYS cc_start: 0.6827 (tppt) cc_final: 0.6542 (tppt) REVERT: B 200 THR cc_start: 0.8544 (m) cc_final: 0.8148 (p) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1580 time to fit residues: 17.8596 Evaluate side-chains 81 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.219728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.189036 restraints weight = 14938.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.193719 restraints weight = 11277.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.196988 restraints weight = 8274.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.199774 restraints weight = 6244.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.200452 restraints weight = 5228.192| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4443 Z= 0.130 Angle : 0.609 5.721 6039 Z= 0.323 Chirality : 0.042 0.133 681 Planarity : 0.006 0.054 779 Dihedral : 6.863 35.053 611 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.92 % Favored : 86.73 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.33), residues: 565 helix: 0.29 (0.53), residues: 99 sheet: -1.86 (0.37), residues: 162 loop : -3.14 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.025 0.002 TYR B 90 PHE 0.014 0.001 PHE B 142 TRP 0.012 0.002 TRP C 186 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4443) covalent geometry : angle 0.60935 ( 6039) hydrogen bonds : bond 0.03640 ( 149) hydrogen bonds : angle 6.23980 ( 390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.6972 (pp) cc_final: 0.6585 (pp) REVERT: B 106 LYS cc_start: 0.7325 (mttt) cc_final: 0.6764 (mptt) REVERT: B 108 ASP cc_start: 0.7639 (t0) cc_final: 0.7075 (m-30) REVERT: B 148 LYS cc_start: 0.6855 (tppt) cc_final: 0.6552 (tppt) REVERT: B 200 THR cc_start: 0.8538 (m) cc_final: 0.8178 (p) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1561 time to fit residues: 16.8540 Evaluate side-chains 79 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.221045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.195636 restraints weight = 14579.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.197206 restraints weight = 11748.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.201099 restraints weight = 10385.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.201612 restraints weight = 6660.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.205739 restraints weight = 5879.431| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4443 Z= 0.132 Angle : 0.601 6.095 6039 Z= 0.319 Chirality : 0.042 0.136 681 Planarity : 0.006 0.054 779 Dihedral : 6.666 34.460 611 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.10 % Favored : 86.55 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.33), residues: 565 helix: 0.41 (0.53), residues: 99 sheet: -1.87 (0.37), residues: 164 loop : -3.03 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.023 0.002 TYR B 90 PHE 0.012 0.001 PHE B 142 TRP 0.015 0.002 TRP C 186 HIS 0.009 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4443) covalent geometry : angle 0.60136 ( 6039) hydrogen bonds : bond 0.03558 ( 149) hydrogen bonds : angle 6.16811 ( 390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.6994 (pp) cc_final: 0.6594 (pp) REVERT: B 106 LYS cc_start: 0.7263 (mttt) cc_final: 0.6683 (mptt) REVERT: B 108 ASP cc_start: 0.7532 (t0) cc_final: 0.7019 (m-30) REVERT: B 148 LYS cc_start: 0.6858 (tppt) cc_final: 0.6621 (tppt) REVERT: B 170 ASP cc_start: 0.3731 (t0) cc_final: 0.3400 (t0) REVERT: B 200 THR cc_start: 0.8478 (m) cc_final: 0.8145 (p) REVERT: C 200 THR cc_start: 0.8624 (p) cc_final: 0.8304 (t) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1623 time to fit residues: 18.3643 Evaluate side-chains 79 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 0.0000 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.223152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.193078 restraints weight = 14700.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.198162 restraints weight = 9870.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.201743 restraints weight = 7314.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.203708 restraints weight = 5772.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.205698 restraints weight = 4891.622| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4443 Z= 0.122 Angle : 0.584 5.130 6039 Z= 0.310 Chirality : 0.042 0.136 681 Planarity : 0.006 0.054 779 Dihedral : 6.482 34.168 611 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.21 % Favored : 87.43 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.33), residues: 565 helix: 0.48 (0.53), residues: 99 sheet: -1.79 (0.37), residues: 164 loop : -2.97 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.023 0.002 TYR B 90 PHE 0.011 0.001 PHE B 142 TRP 0.014 0.002 TRP C 186 HIS 0.007 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4443) covalent geometry : angle 0.58421 ( 6039) hydrogen bonds : bond 0.03449 ( 149) hydrogen bonds : angle 6.07761 ( 390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1615.94 seconds wall clock time: 28 minutes 9.28 seconds (1689.28 seconds total)