Starting phenix.real_space_refine on Wed Mar 12 22:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cr9_16805/03_2025/8cr9_16805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cr9_16805/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cr9_16805/03_2025/8cr9_16805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cr9_16805/03_2025/8cr9_16805.map" model { file = "/net/cci-nas-00/data/ceres_data/8cr9_16805/03_2025/8cr9_16805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cr9_16805/03_2025/8cr9_16805.cif" } resolution = 4.2 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.78, per 1000 atoms: 0.55 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: 2.02 Conformation dependent library (CDL) restraints added in 758.3 milliseconds 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: 0.70 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: 2.51 Time building geometry restraints manager: 2.51 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: 0.300 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: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.520 Find NCS groups from input model: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- 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= 0.859 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 : 0.46 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 (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: -2.67 (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 TRP 0.097 0.026 TRP A 36 HIS 0.017 0.004 HIS A 209 PHE 0.061 0.014 PHE B 212 TYR 0.182 0.034 TYR B 90 ARG 0.009 0.001 ARG B 61 *********************** 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 : 0.629 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: A 17 SER cc_start: 0.8297 (p) cc_final: 0.8090 (m) REVERT: A 163 TRP cc_start: 0.6230 (m100) cc_final: 0.5555 (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: 0.8186 (p) REVERT: B 120 ILE cc_start: 0.3867 (mt) cc_final: 0.3626 (mt) outliers start: 14 outliers final: 8 residues processed: 147 average time/residue: 0.3571 time to fit residues: 64.8004 Evaluate side-chains 110 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4629 r_free = 0.4629 target = 0.233190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.208389 restraints weight = 15603.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.214013 restraints weight = 12837.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.216222 restraints weight = 8483.070| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 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 0.037 4443 Z= 0.258 Angle : 0.806 6.875 6039 Z= 0.436 Chirality : 0.047 0.192 681 Planarity : 0.006 0.046 779 Dihedral : 8.788 40.125 611 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.44 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -2.52 (0.34), residues: 565 helix: -0.21 (0.53), residues: 98 sheet: -1.35 (0.42), residues: 147 loop : -2.39 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 105 HIS 0.005 0.002 HIS A 173 PHE 0.015 0.002 PHE B 142 TYR 0.031 0.003 TYR B 90 ARG 0.006 0.001 ARG A 44 *********************** 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 112 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.662 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: 0.7263 (m-30) cc_final: 0.7057 (m-30) REVERT: A 163 TRP cc_start: 0.5683 (m100) cc_final: 0.5359 (m100) REVERT: B 71 PHE cc_start: 0.5083 (t80) cc_final: 0.4648 (t80) REVERT: B 200 THR cc_start: 0.8357 (m) cc_final: 0.8089 (p) REVERT: C 220 GLU cc_start: 0.6529 (tp30) cc_final: 0.6093 (pm20) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3738 time to fit residues: 51.8278 Evaluate side-chains 95 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN 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 = 0.222274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.192452 restraints weight = 14763.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.196622 restraints weight = 10956.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.200154 restraints weight = 7798.285| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4443 Z= 0.210 Angle : 0.694 5.887 6039 Z= 0.376 Chirality : 0.044 0.150 681 Planarity : 0.006 0.047 779 Dihedral : 7.725 38.588 611 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.04 % Favored : 87.61 % 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 (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: -2.57 (0.34), residues: 565 helix: 0.07 (0.53), residues: 99 sheet: -1.30 (0.42), residues: 151 loop : -2.61 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 186 HIS 0.007 0.002 HIS A 173 PHE 0.016 0.002 PHE B 142 TYR 0.025 0.002 TYR B 90 ARG 0.005 0.001 ARG A 44 *********************** 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 100 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.632 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: A 163 TRP cc_start: 0.5849 (m100) cc_final: 0.5589 (m100) REVERT: B 33 LEU cc_start: 0.7123 (pp) cc_final: 0.6881 (pp) REVERT: B 108 ASP cc_start: 0.7666 (t0) cc_final: 0.7065 (m-30) REVERT: B 170 ASP cc_start: 0.4326 (t0) cc_final: 0.4043 (t0) REVERT: B 200 THR cc_start: 0.8587 (m) cc_final: 0.8266 (p) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4040 time to fit residues: 49.3211 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 : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 173 HIS B 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.221273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.190774 restraints weight = 14638.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.196224 restraints weight = 9612.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.199682 restraints weight = 6984.672| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4443 Z= 0.237 Angle : 0.679 6.449 6039 Z= 0.367 Chirality : 0.043 0.139 681 Planarity : 0.006 0.056 779 Dihedral : 7.500 36.725 611 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.74 % Favored : 86.90 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.76 (0.33), residues: 565 helix: 0.18 (0.53), residues: 99 sheet: -1.57 (0.39), residues: 157 loop : -2.76 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 151 HIS 0.003 0.001 HIS A 173 PHE 0.043 0.002 PHE B 142 TYR 0.028 0.003 TYR B 90 ARG 0.004 0.000 ARG A 44 *********************** 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 101 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.668 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: A 3 GLN cc_start: 0.7578 (mt0) cc_final: 0.7043 (mt0) REVERT: A 163 TRP cc_start: 0.5951 (m100) cc_final: 0.5685 (m100) REVERT: B 33 LEU cc_start: 0.7109 (pp) cc_final: 0.6792 (pp) REVERT: B 108 ASP cc_start: 0.7666 (t0) cc_final: 0.7121 (m-30) REVERT: B 200 THR cc_start: 0.8671 (m) cc_final: 0.8220 (p) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4043 time to fit residues: 49.7126 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** 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 = 0.4518 r_free = 0.4518 target = 0.220379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.189423 restraints weight = 14935.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.194667 restraints weight = 9925.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.198278 restraints weight = 7338.069| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4443 Z= 0.209 Angle : 0.640 5.703 6039 Z= 0.344 Chirality : 0.042 0.137 681 Planarity : 0.006 0.048 779 Dihedral : 7.192 36.127 611 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.39 % Favored : 87.26 % 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 (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: -2.87 (0.33), residues: 565 helix: 0.22 (0.53), residues: 99 sheet: -1.60 (0.40), residues: 152 loop : -2.90 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 105 HIS 0.004 0.001 HIS A 173 PHE 0.032 0.002 PHE B 142 TYR 0.023 0.002 TYR B 90 ARG 0.003 0.000 ARG A 44 *********************** 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 96 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.606 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: A 3 GLN cc_start: 0.7577 (mt0) cc_final: 0.7000 (mt0) REVERT: A 163 TRP cc_start: 0.5978 (m100) cc_final: 0.5730 (m100) REVERT: B 33 LEU cc_start: 0.7003 (pp) cc_final: 0.6787 (pp) REVERT: B 108 ASP cc_start: 0.7649 (t0) cc_final: 0.7050 (m-30) REVERT: B 200 THR cc_start: 0.8482 (m) cc_final: 0.8133 (p) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3724 time to fit residues: 43.9717 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 : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.213537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.188919 restraints weight = 15174.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192120 restraints weight = 12416.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.194438 restraints weight = 9370.752| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4443 Z= 0.367 Angle : 0.793 6.955 6039 Z= 0.427 Chirality : 0.047 0.156 681 Planarity : 0.007 0.059 779 Dihedral : 7.887 35.529 611 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.53 % Allowed : 16.46 % Favored : 83.01 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.42 (0.32), residues: 565 helix: -0.04 (0.51), residues: 99 sheet: -1.74 (0.40), residues: 147 loop : -3.43 (0.29), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 36 HIS 0.003 0.001 HIS A 173 PHE 0.016 0.002 PHE B 87 TYR 0.036 0.004 TYR B 90 ARG 0.007 0.001 ARG A 44 *********************** 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 92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.007 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 33 LEU cc_start: 0.7376 (pp) cc_final: 0.6916 (pp) REVERT: B 106 LYS cc_start: 0.7547 (mttt) cc_final: 0.6920 (mptt) REVERT: B 108 ASP cc_start: 0.7605 (t0) cc_final: 0.7088 (m-30) REVERT: B 200 THR cc_start: 0.8490 (m) cc_final: 0.8144 (p) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4353 time to fit residues: 50.6237 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 : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN B 92 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.217669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.187473 restraints weight = 15175.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192490 restraints weight = 10263.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.195660 restraints weight = 7577.953| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.5705 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= 0.200 Angle : 0.653 5.895 6039 Z= 0.348 Chirality : 0.044 0.136 681 Planarity : 0.006 0.049 779 Dihedral : 7.241 36.110 611 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.57 % Favored : 86.90 % 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 (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: -3.21 (0.33), residues: 565 helix: 0.17 (0.52), residues: 99 sheet: -1.84 (0.38), residues: 158 loop : -3.21 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 105 HIS 0.005 0.001 HIS A 101 PHE 0.021 0.002 PHE A 155 TYR 0.030 0.002 TYR C 177 ARG 0.003 0.000 ARG A 44 *********************** 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 87 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.805 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: B 33 LEU cc_start: 0.7138 (pp) cc_final: 0.6749 (pp) REVERT: B 106 LYS cc_start: 0.7394 (mttt) cc_final: 0.6797 (mptt) REVERT: B 108 ASP cc_start: 0.7589 (t0) cc_final: 0.7019 (m-30) REVERT: B 200 THR cc_start: 0.8600 (m) cc_final: 0.8216 (p) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.5121 time to fit residues: 57.9561 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 : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.218108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.188429 restraints weight = 15200.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.191491 restraints weight = 11750.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.194114 restraints weight = 9258.065| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4443 Z= 0.206 Angle : 0.626 5.896 6039 Z= 0.333 Chirality : 0.043 0.138 681 Planarity : 0.006 0.055 779 Dihedral : 6.986 35.074 611 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.98 % Favored : 85.49 % 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 (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: -3.11 (0.33), residues: 565 helix: 0.32 (0.53), residues: 99 sheet: -1.77 (0.39), residues: 158 loop : -3.17 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 186 HIS 0.007 0.001 HIS A 173 PHE 0.014 0.001 PHE B 142 TYR 0.021 0.002 TYR B 90 ARG 0.004 0.000 ARG A 44 *********************** 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 89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.688 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: 0.7103 (pp) cc_final: 0.6774 (pp) REVERT: B 106 LYS cc_start: 0.7375 (mttt) cc_final: 0.6781 (mptt) REVERT: B 108 ASP cc_start: 0.7612 (t0) cc_final: 0.7018 (m-30) REVERT: B 200 THR cc_start: 0.8539 (m) cc_final: 0.8207 (p) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.4619 time to fit residues: 51.5275 Evaluate side-chains 78 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.218278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.188650 restraints weight = 15155.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.191891 restraints weight = 11257.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.194277 restraints weight = 8919.054| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4443 Z= 0.200 Angle : 0.618 5.854 6039 Z= 0.328 Chirality : 0.043 0.136 681 Planarity : 0.006 0.052 779 Dihedral : 6.862 34.753 611 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.98 % Favored : 85.66 % 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 (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: -3.05 (0.33), residues: 565 helix: 0.34 (0.53), residues: 99 sheet: -1.73 (0.38), residues: 158 loop : -3.13 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 186 HIS 0.007 0.001 HIS A 173 PHE 0.012 0.002 PHE B 142 TYR 0.020 0.002 TYR B 90 ARG 0.003 0.000 ARG A 44 *********************** 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 88 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.677 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: 0.7101 (pp) cc_final: 0.6739 (pp) REVERT: B 106 LYS cc_start: 0.7359 (mttt) cc_final: 0.6775 (mptt) REVERT: B 108 ASP cc_start: 0.7583 (t0) cc_final: 0.6999 (m-30) REVERT: B 200 THR cc_start: 0.8520 (m) cc_final: 0.8182 (p) REVERT: C 200 THR cc_start: 0.8692 (p) cc_final: 0.8306 (t) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3430 time to fit residues: 38.3789 Evaluate side-chains 74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.215423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.184708 restraints weight = 15211.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.187614 restraints weight = 11968.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.190472 restraints weight = 9516.291| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4443 Z= 0.261 Angle : 0.671 6.390 6039 Z= 0.359 Chirality : 0.044 0.136 681 Planarity : 0.006 0.056 779 Dihedral : 7.159 35.078 611 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.93 % Favored : 83.54 % 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 (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: -3.23 (0.33), residues: 565 helix: 0.31 (0.53), residues: 99 sheet: -1.84 (0.38), residues: 158 loop : -3.29 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 186 HIS 0.008 0.002 HIS A 173 PHE 0.011 0.002 PHE B 212 TYR 0.031 0.003 TYR B 90 ARG 0.005 0.001 ARG A 44 ********************** 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 86 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.614 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: A 164 ASN cc_start: 0.3284 (m-40) cc_final: 0.2967 (t0) REVERT: B 33 LEU cc_start: 0.7218 (pp) cc_final: 0.6789 (pp) REVERT: B 106 LYS cc_start: 0.7410 (mttt) cc_final: 0.6845 (mptt) REVERT: B 108 ASP cc_start: 0.7602 (t0) cc_final: 0.7037 (m-30) REVERT: B 148 LYS cc_start: 0.6937 (tppt) cc_final: 0.6600 (tppt) REVERT: B 200 THR cc_start: 0.8534 (m) cc_final: 0.8167 (p) REVERT: C 200 THR cc_start: 0.8711 (p) cc_final: 0.8336 (t) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3255 time to fit residues: 35.6466 Evaluate side-chains 75 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 43 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.219289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.195368 restraints weight = 15243.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.196630 restraints weight = 13350.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.201909 restraints weight = 10711.724| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4443 Z= 0.179 Angle : 0.607 6.134 6039 Z= 0.322 Chirality : 0.042 0.137 681 Planarity : 0.006 0.052 779 Dihedral : 6.797 35.327 611 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.10 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.10 (0.33), residues: 565 helix: 0.43 (0.54), residues: 99 sheet: -1.84 (0.37), residues: 165 loop : -3.17 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 186 HIS 0.002 0.001 HIS B 96 PHE 0.012 0.001 PHE B 142 TYR 0.023 0.002 TYR B 90 ARG 0.003 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.56 seconds wall clock time: 63 minutes 19.04 seconds (3799.04 seconds total)