Starting phenix.real_space_refine on Wed Jul 23 22:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cct_45457/07_2025/9cct_45457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cct_45457/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cct_45457/07_2025/9cct_45457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cct_45457/07_2025/9cct_45457.map" model { file = "/net/cci-nas-00/data/ceres_data/9cct_45457/07_2025/9cct_45457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cct_45457/07_2025/9cct_45457.cif" } resolution = 3.46 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= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.41, per 1000 atoms: 0.76 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: 0.96 Conformation dependent library (CDL) restraints added in 532.8 milliseconds 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: 0.73 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: 1.50 Time building geometry restraints manager: 1.19 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: 0.690 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.720 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- 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 : 11.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (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 TRP 0.014 0.001 TRP C 165 HIS 0.003 0.001 HIS B 40 PHE 0.024 0.002 PHE A 142 TYR 0.011 0.001 TYR A 95 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.17673 ( 140) hydrogen bonds : angle 8.23107 ( 396) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.53517 ( 10) covalent geometry : bond 0.00365 ( 4600) covalent geometry : angle 0.70706 ( 6277) *********************** 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 : 0.497 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: 0.1864 time to fit residues: 22.3027 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 : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.0000 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.4082 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.118513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108006 restraints weight = 6931.116| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.27 r_work: 0.3235 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4605 Z= 0.162 Angle : 0.665 10.307 6287 Z= 0.336 Chirality : 0.046 0.142 711 Planarity : 0.006 0.066 802 Dihedral : 4.903 27.461 637 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.00 % Favored : 90.66 % Rotamer: Outliers : 5.98 % Allowed : 31.87 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.34), residues: 589 helix: -1.22 (1.44), residues: 12 sheet: -0.51 (0.34), residues: 242 loop : -1.85 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 165 HIS 0.004 0.001 HIS C 40 PHE 0.019 0.002 PHE C 111 TYR 0.010 0.001 TYR B 55 ARG 0.001 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 140) hydrogen bonds : angle 6.51590 ( 396) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.48495 ( 10) covalent geometry : bond 0.00377 ( 4600) covalent geometry : angle 0.66488 ( 6277) *********************** 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 126 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.732 Fit side-chains REVERT: A 17 SER cc_start: 0.8529 (t) cc_final: 0.8201 (p) REVERT: A 24 LEU cc_start: 0.8466 (mt) cc_final: 0.8263 (mp) REVERT: A 142 PHE cc_start: 0.7665 (m-80) cc_final: 0.6678 (m-10) REVERT: B 102 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6793 (mp) REVERT: B 172 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6461 (tp40) REVERT: C 111 PHE cc_start: 0.8043 (m-80) cc_final: 0.7732 (m-80) outliers start: 30 outliers final: 15 residues processed: 112 average time/residue: 0.1902 time to fit residues: 27.1914 Evaluate side-chains 110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 A residue 143 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 110 LEU 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 80 SER 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: 1.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.117901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107510 restraints weight = 6867.451| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.23 r_work: 0.3246 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4605 Z= 0.177 Angle : 0.667 10.303 6287 Z= 0.334 Chirality : 0.045 0.141 711 Planarity : 0.005 0.054 802 Dihedral : 4.922 27.586 637 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.34 % Favored : 90.32 % Rotamer: Outliers : 6.37 % Allowed : 32.87 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.34), residues: 589 helix: -1.40 (1.30), residues: 12 sheet: -0.44 (0.34), residues: 242 loop : -1.84 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 41 HIS 0.003 0.001 HIS C 40 PHE 0.028 0.002 PHE C 34 TYR 0.010 0.001 TYR B 97 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 140) hydrogen bonds : angle 6.34101 ( 396) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.47384 ( 10) covalent geometry : bond 0.00405 ( 4600) covalent geometry : angle 0.66753 ( 6277) *********************** 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 125 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.484 Fit side-chains REVERT: A 17 SER cc_start: 0.8420 (t) cc_final: 0.8133 (p) REVERT: A 24 LEU cc_start: 0.8470 (mt) cc_final: 0.8269 (mp) REVERT: A 142 PHE cc_start: 0.7719 (m-80) cc_final: 0.6782 (m-10) REVERT: B 102 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6791 (mp) REVERT: B 172 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.6423 (tp40) REVERT: C 111 PHE cc_start: 0.8163 (m-80) cc_final: 0.7957 (m-80) outliers start: 32 outliers final: 21 residues processed: 111 average time/residue: 0.1632 time to fit residues: 23.0586 Evaluate side-chains 117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 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 170 THR 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 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 193 VAL 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 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.116196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105797 restraints weight = 6921.895| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.24 r_work: 0.3215 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4605 Z= 0.240 Angle : 0.700 10.294 6287 Z= 0.352 Chirality : 0.047 0.148 711 Planarity : 0.005 0.051 802 Dihedral : 5.166 28.630 637 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.51 % Favored : 90.15 % Rotamer: Outliers : 7.77 % Allowed : 31.47 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.34), residues: 589 helix: -1.89 (1.17), residues: 12 sheet: -0.43 (0.34), residues: 242 loop : -1.92 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 41 HIS 0.003 0.001 HIS C 40 PHE 0.028 0.003 PHE C 34 TYR 0.012 0.002 TYR B 55 ARG 0.002 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 140) hydrogen bonds : angle 6.48469 ( 396) SS BOND : bond 0.00240 ( 5) SS BOND : angle 0.61512 ( 10) covalent geometry : bond 0.00535 ( 4600) covalent geometry : angle 0.69985 ( 6277) *********************** 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: 39 poor density : 99 time to evaluate : 0.438 Fit side-chains REVERT: A 24 LEU cc_start: 0.8537 (mt) cc_final: 0.8317 (mp) REVERT: A 142 PHE cc_start: 0.7674 (m-80) cc_final: 0.7003 (m-10) REVERT: B 102 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6810 (mp) REVERT: B 172 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6526 (tp40) REVERT: C 131 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8272 (m) outliers start: 39 outliers final: 28 residues processed: 121 average time/residue: 0.1551 time to fit residues: 23.9121 Evaluate side-chains 130 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 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 196 LYS 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 76 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 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 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.118252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107631 restraints weight = 7032.085| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.32 r_work: 0.3235 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1429 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= 0.171 Angle : 0.675 10.321 6287 Z= 0.336 Chirality : 0.045 0.143 711 Planarity : 0.005 0.047 802 Dihedral : 4.995 28.819 637 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.34 % Favored : 90.32 % Rotamer: Outliers : 7.57 % Allowed : 32.27 % Favored : 60.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.34), residues: 589 helix: -1.92 (1.14), residues: 12 sheet: -0.37 (0.34), residues: 242 loop : -1.90 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 41 HIS 0.003 0.001 HIS C 40 PHE 0.022 0.002 PHE C 34 TYR 0.010 0.001 TYR B 97 ARG 0.002 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 140) hydrogen bonds : angle 6.24660 ( 396) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.50706 ( 10) covalent geometry : bond 0.00391 ( 4600) covalent geometry : angle 0.67538 ( 6277) *********************** 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 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.448 Fit side-chains REVERT: A 24 LEU cc_start: 0.8512 (mt) cc_final: 0.8286 (mp) REVERT: A 142 PHE cc_start: 0.7703 (m-10) cc_final: 0.7071 (m-10) REVERT: B 102 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6785 (mp) REVERT: B 172 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6477 (tp40) REVERT: C 15 GLU cc_start: 0.7972 (tt0) cc_final: 0.7702 (tm-30) REVERT: C 131 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.7977 (t) outliers start: 38 outliers final: 25 residues processed: 119 average time/residue: 0.1559 time to fit residues: 23.8115 Evaluate side-chains 124 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 52 ILE Chi-restraints excluded: chain A residue 57 THR 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 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 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 76 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 193 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 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.0070 chunk 29 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.117832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107496 restraints weight = 6945.514| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.24 r_work: 0.3244 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4605 Z= 0.164 Angle : 0.665 10.302 6287 Z= 0.331 Chirality : 0.045 0.141 711 Planarity : 0.005 0.044 802 Dihedral : 4.880 28.787 637 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.00 % Favored : 90.66 % Rotamer: Outliers : 8.17 % Allowed : 32.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.34), residues: 589 helix: -1.81 (1.16), residues: 12 sheet: -0.29 (0.34), residues: 242 loop : -1.89 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 PHE 0.019 0.002 PHE C 34 TYR 0.010 0.001 TYR B 97 ARG 0.001 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 140) hydrogen bonds : angle 6.14023 ( 396) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.53258 ( 10) covalent geometry : bond 0.00375 ( 4600) covalent geometry : angle 0.66475 ( 6277) *********************** 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 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.509 Fit side-chains REVERT: A 24 LEU cc_start: 0.8506 (mt) cc_final: 0.8277 (mp) REVERT: A 142 PHE cc_start: 0.7721 (m-10) cc_final: 0.7029 (m-10) REVERT: B 102 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6740 (mp) REVERT: B 172 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6383 (tp40) REVERT: C 131 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.7939 (t) outliers start: 41 outliers final: 32 residues processed: 122 average time/residue: 0.1579 time to fit residues: 24.6793 Evaluate side-chains 129 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 15 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 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 196 LYS Chi-restraints excluded: chain B residue 200 CYS 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 45 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 76 THR 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 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 11 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.116057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105801 restraints weight = 6929.258| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.24 r_work: 0.3203 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4605 Z= 0.271 Angle : 0.731 10.272 6287 Z= 0.365 Chirality : 0.048 0.147 711 Planarity : 0.005 0.044 802 Dihedral : 5.234 29.806 637 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.51 % Favored : 90.15 % Rotamer: Outliers : 8.57 % Allowed : 32.27 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.34), residues: 589 helix: -2.21 (1.06), residues: 12 sheet: -0.43 (0.34), residues: 247 loop : -1.99 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 154 HIS 0.004 0.001 HIS C 40 PHE 0.034 0.003 PHE C 34 TYR 0.012 0.002 TYR B 55 ARG 0.003 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 140) hydrogen bonds : angle 6.49502 ( 396) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.72944 ( 10) covalent geometry : bond 0.00600 ( 4600) covalent geometry : angle 0.73118 ( 6277) *********************** 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 141 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.483 Fit side-chains REVERT: A 142 PHE cc_start: 0.7775 (m-10) cc_final: 0.7206 (m-10) REVERT: B 40 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.8159 (m90) REVERT: B 102 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6589 (mp) REVERT: B 172 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.6507 (tp40) REVERT: C 15 GLU cc_start: 0.7978 (tt0) cc_final: 0.7579 (tm-30) REVERT: C 131 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8256 (t) outliers start: 43 outliers final: 34 residues processed: 125 average time/residue: 0.1510 time to fit residues: 24.2748 Evaluate side-chains 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 64 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 121 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.1980 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.117783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107564 restraints weight = 6928.070| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.24 r_work: 0.3245 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4605 Z= 0.152 Angle : 0.688 11.008 6287 Z= 0.336 Chirality : 0.046 0.153 711 Planarity : 0.005 0.043 802 Dihedral : 4.933 29.376 637 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.98 % Favored : 91.68 % Rotamer: Outliers : 6.97 % Allowed : 33.86 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.34), residues: 589 helix: -2.02 (1.13), residues: 12 sheet: -0.25 (0.35), residues: 242 loop : -1.91 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 165 HIS 0.002 0.001 HIS C 40 PHE 0.030 0.002 PHE C 34 TYR 0.010 0.001 TYR C 107 ARG 0.001 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 140) hydrogen bonds : angle 6.11127 ( 396) SS BOND : bond 0.00229 ( 5) SS BOND : angle 0.54923 ( 10) covalent geometry : bond 0.00349 ( 4600) covalent geometry : angle 0.68866 ( 6277) *********************** 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 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.602 Fit side-chains REVERT: A 142 PHE cc_start: 0.7762 (m-10) cc_final: 0.7066 (m-10) REVERT: B 73 SER cc_start: 0.8203 (p) cc_final: 0.7997 (t) REVERT: B 102 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6488 (mp) REVERT: C 15 GLU cc_start: 0.7912 (tt0) cc_final: 0.7494 (tm-30) REVERT: C 131 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8105 (t) REVERT: C 203 GLN cc_start: 0.8525 (tp-100) cc_final: 0.8191 (tm-30) outliers start: 35 outliers final: 31 residues processed: 120 average time/residue: 0.1544 time to fit residues: 24.1529 Evaluate side-chains 132 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 76 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 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 29 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.117767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107483 restraints weight = 6812.380| |-----------------------------------------------------------------------------| 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: 4.39 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1672 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= 0.166 Angle : 0.681 10.258 6287 Z= 0.335 Chirality : 0.046 0.145 711 Planarity : 0.005 0.044 802 Dihedral : 4.923 28.871 637 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.17 % Favored : 90.49 % Rotamer: Outliers : 7.17 % Allowed : 33.67 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.35), residues: 589 helix: -2.04 (1.14), residues: 12 sheet: -0.37 (0.34), residues: 248 loop : -1.86 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 PHE 0.028 0.002 PHE C 34 TYR 0.010 0.001 TYR C 107 ARG 0.001 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 140) hydrogen bonds : angle 6.08738 ( 396) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.58104 ( 10) covalent geometry : bond 0.00379 ( 4600) covalent geometry : angle 0.68156 ( 6277) *********************** 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 134 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.495 Fit side-chains REVERT: A 142 PHE cc_start: 0.7745 (m-10) cc_final: 0.7048 (m-10) REVERT: B 102 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6488 (mp) REVERT: C 15 GLU cc_start: 0.7838 (tt0) cc_final: 0.7437 (tm-30) REVERT: C 131 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8188 (t) outliers start: 36 outliers final: 31 residues processed: 120 average time/residue: 0.1569 time to fit residues: 24.2532 Evaluate side-chains 131 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 126 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 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 207 LEU 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 121 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 193 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 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 43 optimal weight: 0.3980 chunk 10 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.117822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107526 restraints weight = 6901.664| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.24 r_work: 0.3226 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1719 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= 0.162 Angle : 0.681 10.229 6287 Z= 0.334 Chirality : 0.046 0.139 711 Planarity : 0.005 0.044 802 Dihedral : 4.904 28.786 637 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.66 % Favored : 91.00 % Rotamer: Outliers : 7.37 % Allowed : 33.47 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.35), residues: 589 helix: -1.96 (1.19), residues: 12 sheet: -0.25 (0.34), residues: 243 loop : -1.86 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 165 HIS 0.004 0.001 HIS C 40 PHE 0.028 0.002 PHE C 34 TYR 0.010 0.001 TYR C 65 ARG 0.001 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 140) hydrogen bonds : angle 6.01987 ( 396) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.58342 ( 10) covalent geometry : bond 0.00371 ( 4600) covalent geometry : angle 0.68106 ( 6277) ********************** 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 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.516 Fit side-chains REVERT: A 33 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8283 (t0) REVERT: A 142 PHE cc_start: 0.7814 (m-10) cc_final: 0.7176 (m-10) REVERT: B 73 SER cc_start: 0.8228 (p) cc_final: 0.8023 (t) REVERT: B 102 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6436 (mp) REVERT: C 131 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8213 (t) REVERT: C 203 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8250 (tm-30) outliers start: 37 outliers final: 34 residues processed: 123 average time/residue: 0.1545 time to fit residues: 24.3913 Evaluate side-chains 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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 B residue 207 LEU 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 132 VAL Chi-restraints excluded: chain C residue 193 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 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.118073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107819 restraints weight = 6858.502| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.23 r_work: 0.3228 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1760 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= 0.170 Angle : 0.690 10.203 6287 Z= 0.342 Chirality : 0.046 0.147 711 Planarity : 0.005 0.044 802 Dihedral : 4.946 28.837 637 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.68 % Favored : 89.98 % Rotamer: Outliers : 7.97 % Allowed : 33.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.35), residues: 589 helix: -1.99 (1.18), residues: 12 sheet: -0.34 (0.34), residues: 248 loop : -1.83 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 165 HIS 0.003 0.001 HIS C 40 PHE 0.034 0.002 PHE C 34 TYR 0.011 0.001 TYR B 97 ARG 0.001 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 140) hydrogen bonds : angle 6.01337 ( 396) SS BOND : bond 0.00238 ( 5) SS BOND : angle 0.57750 ( 10) covalent geometry : bond 0.00389 ( 4600) covalent geometry : angle 0.69049 ( 6277) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.36 seconds wall clock time: 44 minutes 51.45 seconds (2691.45 seconds total)