Starting phenix.real_space_refine on Wed Sep 17 04:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cct_45457/09_2025/9cct_45457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cct_45457/09_2025/9cct_45457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cct_45457/09_2025/9cct_45457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cct_45457/09_2025/9cct_45457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cct_45457/09_2025/9cct_45457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cct_45457/09_2025/9cct_45457.map" } resolution = 3.46 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2837 2.51 5 N 743 2.21 5 O 894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4489 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1196 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 148} Chain: "B" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1625 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 207} Time building chain proxies: 1.31, per 1000 atoms: 0.29 Number of scatterers: 4489 At special positions: 0 Unit cell: (72.224, 68.672, 110.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 894 8.00 N 743 7.00 C 2837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 207 " distance=2.04 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: 0.39 Conformation dependent library (CDL) restraints added in 175.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 16 sheets defined 6.4% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.687A pdb=" N SER A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.808A pdb=" N ALA B 89 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 removed outlier: 3.819A pdb=" N SER B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.928A pdb=" N TYR C 37 " --> pdb=" O PHE C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.780A pdb=" N SER C 96 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.504A pdb=" N CYS A 3 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 22 removed outlier: 3.527A pdb=" N ASN A 147 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 150 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 125 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 60 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG A 132 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU A 58 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR A 134 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 56 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.652A pdb=" N GLY A 73 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 120 removed outlier: 6.604A pdb=" N VAL A 154 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.897A pdb=" N TYR B 77 " --> pdb=" O CYS B 28 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 75 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 25 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 60 removed outlier: 5.590A pdb=" N LEU B 52 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 121 through 124 removed outlier: 5.709A pdb=" N VAL B 139 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU B 185 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU B 141 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER B 183 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN B 143 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B 181 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.562A pdb=" N VAL B 202 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 211 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.589A pdb=" N VAL C 23 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.528A pdb=" N GLN C 87 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 74 " --> pdb=" O GLN C 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.689A pdb=" N GLU C 15 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS C 43 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TRP C 52 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.689A pdb=" N GLU C 15 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 113 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 135 removed outlier: 3.820A pdb=" N VAL C 195 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 155 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR C 187 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 131 through 135 removed outlier: 3.820A pdb=" N VAL C 195 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 155 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR C 187 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 165 163 hydrogen bonds defined for protein. 396 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: 0.74 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1424 1.34 - 1.46: 1130 1.46 - 1.58: 2026 1.58 - 1.70: 1 1.70 - 1.81: 19 Bond restraints: 4600 Sorted by residual: bond pdb=" CB PRO A 157 " pdb=" CG PRO A 157 " ideal model delta sigma weight residual 1.492 1.623 -0.131 5.00e-02 4.00e+02 6.85e+00 bond pdb=" C PHE B 124 " pdb=" O PHE B 124 " ideal model delta sigma weight residual 1.238 1.252 -0.015 1.28e-02 6.10e+03 1.29e+00 bond pdb=" CA GLU B 193 " pdb=" CB GLU B 193 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.21e-02 6.83e+03 8.47e-01 bond pdb=" C THR A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.25e-02 6.40e+03 8.08e-01 bond pdb=" CB PRO C 160 " pdb=" CG PRO C 160 " ideal model delta sigma weight residual 1.506 1.538 -0.032 3.90e-02 6.57e+02 6.89e-01 ... (remaining 4595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 6147 2.10 - 4.20: 109 4.20 - 6.30: 17 6.30 - 8.40: 1 8.40 - 10.50: 3 Bond angle restraints: 6277 Sorted by residual: angle pdb=" CA PRO A 157 " pdb=" N PRO A 157 " pdb=" CD PRO A 157 " ideal model delta sigma weight residual 112.00 102.55 9.45 1.40e+00 5.10e-01 4.56e+01 angle pdb=" C SER B 99 " pdb=" N TYR B 100 " pdb=" CA TYR B 100 " ideal model delta sigma weight residual 121.80 132.30 -10.50 2.44e+00 1.68e-01 1.85e+01 angle pdb=" CA LYS C 225 " pdb=" CB LYS C 225 " pdb=" CG LYS C 225 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N PRO A 157 " pdb=" CD PRO A 157 " pdb=" CG PRO A 157 " ideal model delta sigma weight residual 103.20 98.03 5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 110.69 116.84 -6.15 2.05e+00 2.38e-01 9.00e+00 ... (remaining 6272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2281 17.09 - 34.19: 334 34.19 - 51.28: 83 51.28 - 68.37: 17 68.37 - 85.46: 10 Dihedral angle restraints: 2725 sinusoidal: 1006 harmonic: 1719 Sorted by residual: dihedral pdb=" CA ASN C 66 " pdb=" C ASN C 66 " pdb=" N GLN C 67 " pdb=" CA GLN C 67 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CB CYS C 151 " pdb=" SG CYS C 151 " pdb=" SG CYS C 207 " pdb=" CB CYS C 207 " ideal model delta sinusoidal sigma weight residual 93.00 120.54 -27.54 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CA TYR C 65 " pdb=" C TYR C 65 " pdb=" N ASN C 66 " pdb=" CA ASN C 66 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 382 0.029 - 0.059: 209 0.059 - 0.088: 60 0.088 - 0.118: 50 0.118 - 0.147: 10 Chirality restraints: 711 Sorted by residual: chirality pdb=" CA VAL B 116 " pdb=" N VAL B 116 " pdb=" C VAL B 116 " pdb=" CB VAL B 116 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE B 15 " pdb=" N ILE B 15 " pdb=" C ILE B 15 " pdb=" CB ILE B 15 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 708 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 156 " 0.083 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 157 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 45 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO C 46 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 46 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 46 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 57 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 58 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.024 5.00e-02 4.00e+02 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 125 2.68 - 3.23: 4219 3.23 - 3.79: 6820 3.79 - 4.34: 9300 4.34 - 4.90: 15547 Nonbonded interactions: 36011 Sorted by model distance: nonbonded pdb=" O VAL B 34 " pdb=" OH TYR B 77 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR A 95 " pdb=" O PRO A 102 " model vdw 2.205 3.040 nonbonded pdb=" O LYS A 121 " pdb=" OG SER A 124 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" OD1 ASN C 38 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 42 " pdb=" OE1 GLN B 95 " model vdw 2.295 3.040 ... (remaining 36006 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.610 Find NCS groups from input model: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 4605 Z= 0.149 Angle : 0.707 10.498 6287 Z= 0.373 Chirality : 0.045 0.147 711 Planarity : 0.007 0.120 802 Dihedral : 17.895 85.465 1616 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.98 % Favored : 91.68 % Rotamer: Outliers : 0.20 % Allowed : 37.05 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.79 (0.35), residues: 589 helix: -1.60 (1.00), residues: 18 sheet: -0.51 (0.35), residues: 242 loop : -1.72 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.011 0.001 TYR A 95 PHE 0.024 0.002 PHE A 142 TRP 0.014 0.001 TRP C 165 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4600) covalent geometry : angle 0.70706 ( 6277) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.53517 ( 10) hydrogen bonds : bond 0.17673 ( 140) hydrogen bonds : angle 8.23107 ( 396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.167 Fit side-chains REVERT: C 128 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8562 (ttpp) REVERT: C 203 GLN cc_start: 0.8471 (tp-100) cc_final: 0.8155 (tm-30) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0824 time to fit residues: 9.9309 Evaluate side-chains 94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 40 HIS B 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106419 restraints weight = 7090.992| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.21 r_work: 0.3213 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4605 Z= 0.281 Angle : 0.733 10.303 6287 Z= 0.374 Chirality : 0.048 0.150 711 Planarity : 0.006 0.068 802 Dihedral : 5.350 28.835 637 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.19 % Favored : 89.47 % Rotamer: Outliers : 7.77 % Allowed : 31.87 % Favored : 60.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -2.02 (0.34), residues: 589 helix: -1.75 (1.29), residues: 12 sheet: -0.58 (0.34), residues: 241 loop : -1.96 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.011 0.002 TYR B 55 PHE 0.028 0.003 PHE C 111 TRP 0.013 0.002 TRP B 41 HIS 0.005 0.002 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00628 ( 4600) covalent geometry : angle 0.73310 ( 6277) SS BOND : bond 0.00293 ( 5) SS BOND : angle 0.64300 ( 10) hydrogen bonds : bond 0.04270 ( 140) hydrogen bonds : angle 6.91796 ( 396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.157 Fit side-chains REVERT: A 17 SER cc_start: 0.8488 (t) cc_final: 0.8180 (p) REVERT: A 142 PHE cc_start: 0.7781 (m-80) cc_final: 0.6780 (m-10) REVERT: B 22 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: B 78 SER cc_start: 0.8630 (t) cc_final: 0.8378 (p) REVERT: B 102 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6837 (mp) REVERT: B 172 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6637 (tp40) REVERT: C 33 THR cc_start: 0.8661 (p) cc_final: 0.8321 (p) REVERT: C 55 THR cc_start: 0.8282 (p) cc_final: 0.8011 (t) REVERT: C 131 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8171 (t) outliers start: 39 outliers final: 21 residues processed: 130 average time/residue: 0.0664 time to fit residues: 11.0908 Evaluate side-chains 124 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106723 restraints weight = 6893.263| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.21 r_work: 0.3230 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4605 Z= 0.196 Angle : 0.689 10.339 6287 Z= 0.347 Chirality : 0.046 0.183 711 Planarity : 0.006 0.057 802 Dihedral : 5.133 29.413 637 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.00 % Favored : 90.66 % Rotamer: Outliers : 6.37 % Allowed : 33.67 % Favored : 59.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.94 (0.34), residues: 589 helix: -1.86 (1.17), residues: 12 sheet: -0.50 (0.34), residues: 242 loop : -1.93 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.009 0.002 TYR B 55 PHE 0.028 0.002 PHE C 34 TRP 0.009 0.001 TRP C 165 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 4600) covalent geometry : angle 0.68910 ( 6277) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.49366 ( 10) hydrogen bonds : bond 0.03735 ( 140) hydrogen bonds : angle 6.56401 ( 396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.125 Fit side-chains REVERT: A 142 PHE cc_start: 0.7793 (m-80) cc_final: 0.6900 (m-10) REVERT: B 78 SER cc_start: 0.8561 (t) cc_final: 0.8348 (p) REVERT: B 102 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6775 (mp) REVERT: B 172 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6550 (tp40) outliers start: 32 outliers final: 19 residues processed: 116 average time/residue: 0.0737 time to fit residues: 10.8703 Evaluate side-chains 119 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 45 HIS C 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107156 restraints weight = 6889.889| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.24 r_work: 0.3223 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4605 Z= 0.200 Angle : 0.688 10.323 6287 Z= 0.345 Chirality : 0.046 0.149 711 Planarity : 0.005 0.051 802 Dihedral : 5.096 29.275 637 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.83 % Favored : 90.83 % Rotamer: Outliers : 7.97 % Allowed : 32.27 % Favored : 59.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.91 (0.34), residues: 589 helix: -1.92 (1.17), residues: 12 sheet: -0.42 (0.34), residues: 242 loop : -1.95 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.010 0.002 TYR B 55 PHE 0.019 0.002 PHE C 34 TRP 0.008 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 4600) covalent geometry : angle 0.68817 ( 6277) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.54798 ( 10) hydrogen bonds : bond 0.03614 ( 140) hydrogen bonds : angle 6.47800 ( 396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.179 Fit side-chains REVERT: A 142 PHE cc_start: 0.7698 (m-80) cc_final: 0.6980 (m-10) REVERT: B 102 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6805 (mp) REVERT: B 172 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.6537 (tp40) REVERT: C 131 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8033 (t) outliers start: 40 outliers final: 28 residues processed: 124 average time/residue: 0.0668 time to fit residues: 10.7657 Evaluate side-chains 123 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.4980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107817 restraints weight = 6952.943| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.26 r_work: 0.3240 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4605 Z= 0.165 Angle : 0.666 10.301 6287 Z= 0.332 Chirality : 0.045 0.147 711 Planarity : 0.005 0.048 802 Dihedral : 4.945 29.194 637 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.00 % Favored : 90.66 % Rotamer: Outliers : 8.96 % Allowed : 31.47 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.85 (0.34), residues: 589 helix: -1.96 (1.12), residues: 12 sheet: -0.36 (0.34), residues: 242 loop : -1.93 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.009 0.001 TYR B 97 PHE 0.019 0.002 PHE C 111 TRP 0.007 0.001 TRP C 165 HIS 0.002 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4600) covalent geometry : angle 0.66662 ( 6277) SS BOND : bond 0.00240 ( 5) SS BOND : angle 0.52170 ( 10) hydrogen bonds : bond 0.03394 ( 140) hydrogen bonds : angle 6.27292 ( 396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.161 Fit side-chains REVERT: A 142 PHE cc_start: 0.7727 (m-10) cc_final: 0.7068 (m-10) REVERT: B 102 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6761 (mp) REVERT: B 172 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6441 (tp40) REVERT: C 131 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.7995 (t) outliers start: 45 outliers final: 32 residues processed: 126 average time/residue: 0.0637 time to fit residues: 10.4790 Evaluate side-chains 130 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.0030 chunk 34 optimal weight: 0.8980 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107148 restraints weight = 6982.071| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.26 r_work: 0.3238 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4605 Z= 0.170 Angle : 0.664 10.243 6287 Z= 0.330 Chirality : 0.045 0.144 711 Planarity : 0.005 0.046 802 Dihedral : 4.906 28.748 637 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.17 % Favored : 90.49 % Rotamer: Outliers : 8.96 % Allowed : 31.47 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.78 (0.34), residues: 589 helix: -1.93 (1.15), residues: 12 sheet: -0.31 (0.34), residues: 242 loop : -1.88 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.010 0.001 TYR B 97 PHE 0.033 0.002 PHE C 34 TRP 0.006 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4600) covalent geometry : angle 0.66410 ( 6277) SS BOND : bond 0.00321 ( 5) SS BOND : angle 0.58062 ( 10) hydrogen bonds : bond 0.03339 ( 140) hydrogen bonds : angle 6.21244 ( 396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 0.167 Fit side-chains REVERT: A 142 PHE cc_start: 0.7761 (m-10) cc_final: 0.7123 (m-10) REVERT: B 40 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7988 (m90) REVERT: B 102 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6722 (mp) REVERT: B 172 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6382 (tp40) REVERT: C 131 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.7988 (t) outliers start: 45 outliers final: 36 residues processed: 124 average time/residue: 0.0646 time to fit residues: 10.4594 Evaluate side-chains 134 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107319 restraints weight = 6946.184| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.23 r_work: 0.3239 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4605 Z= 0.168 Angle : 0.675 10.257 6287 Z= 0.331 Chirality : 0.046 0.143 711 Planarity : 0.005 0.044 802 Dihedral : 4.878 28.958 637 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.83 % Favored : 90.83 % Rotamer: Outliers : 8.37 % Allowed : 32.27 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.77 (0.34), residues: 589 helix: -1.95 (1.14), residues: 12 sheet: -0.30 (0.34), residues: 242 loop : -1.88 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.010 0.001 TYR B 97 PHE 0.026 0.002 PHE C 34 TRP 0.006 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4600) covalent geometry : angle 0.67489 ( 6277) SS BOND : bond 0.00245 ( 5) SS BOND : angle 0.57302 ( 10) hydrogen bonds : bond 0.03311 ( 140) hydrogen bonds : angle 6.18055 ( 396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.179 Fit side-chains REVERT: A 142 PHE cc_start: 0.7765 (m-10) cc_final: 0.7087 (m-10) REVERT: B 40 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.8024 (m90) REVERT: B 73 SER cc_start: 0.8220 (p) cc_final: 0.8012 (t) REVERT: B 102 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6570 (mp) REVERT: B 172 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.6366 (tp40) REVERT: C 131 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.7993 (t) outliers start: 42 outliers final: 32 residues processed: 120 average time/residue: 0.0673 time to fit residues: 10.3820 Evaluate side-chains 130 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.0070 chunk 42 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106921 restraints weight = 7018.482| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.24 r_work: 0.3232 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4605 Z= 0.183 Angle : 0.710 11.259 6287 Z= 0.344 Chirality : 0.046 0.174 711 Planarity : 0.005 0.043 802 Dihedral : 4.926 29.121 637 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.00 % Favored : 90.66 % Rotamer: Outliers : 8.17 % Allowed : 33.07 % Favored : 58.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.76 (0.34), residues: 589 helix: -1.95 (1.18), residues: 12 sheet: -0.30 (0.35), residues: 242 loop : -1.87 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.010 0.001 TYR B 97 PHE 0.024 0.002 PHE C 34 TRP 0.006 0.001 TRP C 165 HIS 0.002 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 4600) covalent geometry : angle 0.70996 ( 6277) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.58371 ( 10) hydrogen bonds : bond 0.03353 ( 140) hydrogen bonds : angle 6.20047 ( 396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.165 Fit side-chains REVERT: A 142 PHE cc_start: 0.7780 (m-10) cc_final: 0.7155 (m-10) REVERT: B 40 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8028 (m90) REVERT: B 73 SER cc_start: 0.8216 (p) cc_final: 0.8003 (t) REVERT: B 102 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6525 (mp) REVERT: B 172 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6366 (tp40) REVERT: C 131 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8144 (t) outliers start: 41 outliers final: 33 residues processed: 121 average time/residue: 0.0707 time to fit residues: 10.9570 Evaluate side-chains 130 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.0040 chunk 12 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 45 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107527 restraints weight = 6993.180| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.23 r_work: 0.3244 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4605 Z= 0.169 Angle : 0.694 10.203 6287 Z= 0.338 Chirality : 0.046 0.153 711 Planarity : 0.005 0.042 802 Dihedral : 4.889 28.904 637 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.83 % Favored : 90.83 % Rotamer: Outliers : 8.37 % Allowed : 33.27 % Favored : 58.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.75 (0.34), residues: 589 helix: -1.96 (1.18), residues: 12 sheet: -0.28 (0.35), residues: 242 loop : -1.87 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.010 0.001 TYR B 97 PHE 0.023 0.002 PHE C 34 TRP 0.006 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4600) covalent geometry : angle 0.69399 ( 6277) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.55066 ( 10) hydrogen bonds : bond 0.03263 ( 140) hydrogen bonds : angle 6.13739 ( 396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.164 Fit side-chains REVERT: A 142 PHE cc_start: 0.7744 (m-10) cc_final: 0.7112 (m-10) REVERT: B 73 SER cc_start: 0.8214 (p) cc_final: 0.8004 (t) REVERT: B 102 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6450 (mp) REVERT: B 172 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6467 (tp40) REVERT: C 131 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8187 (t) REVERT: C 203 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8216 (tm-30) outliers start: 42 outliers final: 36 residues processed: 125 average time/residue: 0.0661 time to fit residues: 10.6615 Evaluate side-chains 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 45 HIS B 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106619 restraints weight = 6990.688| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.22 r_work: 0.3226 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4605 Z= 0.218 Angle : 0.714 10.201 6287 Z= 0.350 Chirality : 0.047 0.142 711 Planarity : 0.005 0.044 802 Dihedral : 5.026 29.125 637 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.34 % Favored : 90.32 % Rotamer: Outliers : 7.97 % Allowed : 33.86 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.77 (0.34), residues: 589 helix: -2.04 (1.16), residues: 12 sheet: -0.30 (0.35), residues: 243 loop : -1.88 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.012 0.002 TYR B 97 PHE 0.023 0.003 PHE C 111 TRP 0.008 0.001 TRP B 154 HIS 0.004 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4600) covalent geometry : angle 0.71400 ( 6277) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.72173 ( 10) hydrogen bonds : bond 0.03475 ( 140) hydrogen bonds : angle 6.27366 ( 396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.172 Fit side-chains REVERT: A 142 PHE cc_start: 0.7782 (m-10) cc_final: 0.7169 (m-10) REVERT: B 73 SER cc_start: 0.8213 (p) cc_final: 0.7988 (t) REVERT: B 102 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6501 (mp) REVERT: B 172 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6434 (tp40) REVERT: C 131 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8269 (t) REVERT: C 203 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8191 (tm-30) outliers start: 40 outliers final: 36 residues processed: 121 average time/residue: 0.0648 time to fit residues: 10.1125 Evaluate side-chains 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108397 restraints weight = 7002.371| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.30 r_work: 0.3240 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4605 Z= 0.157 Angle : 0.691 10.206 6287 Z= 0.337 Chirality : 0.046 0.141 711 Planarity : 0.005 0.043 802 Dihedral : 4.927 28.941 637 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.98 % Favored : 91.68 % Rotamer: Outliers : 7.17 % Allowed : 34.66 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.73 (0.34), residues: 589 helix: -1.94 (1.22), residues: 12 sheet: -0.29 (0.34), residues: 243 loop : -1.84 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.010 0.001 TYR B 97 PHE 0.023 0.002 PHE C 34 TRP 0.007 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4600) covalent geometry : angle 0.69132 ( 6277) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.59525 ( 10) hydrogen bonds : bond 0.03232 ( 140) hydrogen bonds : angle 6.09008 ( 396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1284.10 seconds wall clock time: 22 minutes 47.43 seconds (1367.43 seconds total)