Starting phenix.real_space_refine on Tue Aug 4 18:33:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rug_54271/08_2026/9rug_54271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rug_54271/08_2026/9rug_54271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rug_54271/08_2026/9rug_54271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rug_54271/08_2026/9rug_54271.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rug_54271/08_2026/9rug_54271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rug_54271/08_2026/9rug_54271.map" } resolution = 2.74 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= 0.005 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 21 5.16 5 C 3728 2.51 5 N 984 2.21 5 O 1129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5862 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1489 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 10, 'TRANS': 186} Chain breaks: 3 Chain: "L" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1443 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 3 Chain: "B" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1411 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain breaks: 2 Chain: "A" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1459 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain: "P" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.33, per 1000 atoms: 0.23 Number of scatterers: 5862 At special positions: 0 Unit cell: (62.73, 84.15, 126.99, 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 21 16.00 O 1129 8.00 N 984 7.00 C 3728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 165 " distance=2.03 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: 0.28 Conformation dependent library (CDL) restraints added in 194.2 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1410 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 16 sheets defined 12.0% alpha, 45.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.558A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.514A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 53 through 64 removed outlier: 4.438A pdb=" N ASP B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.941A pdb=" N LEU B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'A' and resid 48 through 53 removed outlier: 4.181A pdb=" N ARG A 53 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 79 removed outlier: 3.979A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.009A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.836A pdb=" N CYS H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.312A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 162 through 163 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.625A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.686A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 146 through 150 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 removed outlier: 4.939A pdb=" N GLU B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR B 32 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR B 9 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 15 " --> pdb=" O TYR B 9 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE B 11 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 13 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY B 13 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 12 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A 26 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 14 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN A 24 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR A 16 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 22 " --> pdb=" O TYR A 16 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N GLY A 23 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASP A 38 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE A 25 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR A 36 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS A 27 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 103 Processing sheet with id=AB3, first strand: chain 'B' and resid 98 through 103 Processing sheet with id=AB4, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'A' and resid 90 through 95 Processing sheet with id=AB6, first strand: chain 'A' and resid 90 through 95 Processing sheet with id=AB7, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.585A pdb=" N TRP A 123 " --> pdb=" O VAL A 130 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 717 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: 0.68 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1869 1.34 - 1.46: 1078 1.46 - 1.57: 3030 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 6004 Sorted by residual: bond pdb=" CA GLU H 157 " pdb=" C GLU H 157 " ideal model delta sigma weight residual 1.520 1.557 -0.037 1.23e-02 6.61e+03 9.00e+00 bond pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.28e-02 6.10e+03 2.35e+00 bond pdb=" CA THR H 160 " pdb=" CB THR H 160 " ideal model delta sigma weight residual 1.524 1.547 -0.022 1.46e-02 4.69e+03 2.33e+00 bond pdb=" C ILE L 48 " pdb=" O ILE L 48 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.13e-02 7.83e+03 2.32e+00 bond pdb=" CA LEU L 33 " pdb=" C LEU L 33 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.21e-02 6.83e+03 2.19e+00 ... (remaining 5999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 7863 1.92 - 3.85: 223 3.85 - 5.77: 65 5.77 - 7.70: 16 7.70 - 9.62: 7 Bond angle restraints: 8174 Sorted by residual: angle pdb=" N ASP B 152 " pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 112.26 105.71 6.55 1.32e+00 5.74e-01 2.46e+01 angle pdb=" N ASP B 121 " pdb=" CA ASP B 121 " pdb=" C ASP B 121 " ideal model delta sigma weight residual 111.28 117.75 -6.47 1.35e+00 5.49e-01 2.29e+01 angle pdb=" N GLN B 126 " pdb=" CA GLN B 126 " pdb=" C GLN B 126 " ideal model delta sigma weight residual 107.41 97.79 9.62 2.02e+00 2.45e-01 2.27e+01 angle pdb=" C TYR L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta sigma weight residual 119.05 113.84 5.21 1.11e+00 8.12e-01 2.20e+01 angle pdb=" C PHE H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta sigma weight residual 119.76 115.05 4.71 1.03e+00 9.43e-01 2.09e+01 ... (remaining 8169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 3132 17.44 - 34.89: 325 34.89 - 52.33: 73 52.33 - 69.78: 21 69.78 - 87.22: 13 Dihedral angle restraints: 3564 sinusoidal: 1387 harmonic: 2177 Sorted by residual: dihedral pdb=" CA ASP B 135 " pdb=" C ASP B 135 " pdb=" N GLN B 136 " pdb=" CA GLN B 136 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C GLU H 157 " pdb=" N GLU H 157 " pdb=" CA GLU H 157 " pdb=" CB GLU H 157 " ideal model delta harmonic sigma weight residual -122.60 -133.01 10.41 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" CA TYR A 11 " pdb=" C TYR A 11 " pdb=" N GLY A 12 " pdb=" CA GLY A 12 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 3561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 779 0.073 - 0.145: 131 0.145 - 0.218: 7 0.218 - 0.290: 3 0.290 - 0.363: 4 Chirality restraints: 924 Sorted by residual: chirality pdb=" CA PHE H 155 " pdb=" N PHE H 155 " pdb=" C PHE H 155 " pdb=" CB PHE H 155 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ASP B 121 " pdb=" N ASP B 121 " pdb=" C ASP B 121 " pdb=" CB ASP B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA TYR B 123 " pdb=" N TYR B 123 " pdb=" C TYR B 123 " pdb=" CB TYR B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 921 not shown) Planarity restraints: 1043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 20 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 21 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 123 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO B 124 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 157 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO H 158 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 158 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 158 " -0.036 5.00e-02 4.00e+02 ... (remaining 1040 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 371 2.73 - 3.27: 5674 3.27 - 3.81: 10025 3.81 - 4.36: 11800 4.36 - 4.90: 20666 Nonbonded interactions: 48536 Sorted by model distance: nonbonded pdb=" N GLU H 89 " pdb=" OE1 GLU H 89 " model vdw 2.185 3.120 nonbonded pdb=" OD1 ASP L 17 " pdb=" N ARG L 18 " model vdw 2.210 3.120 nonbonded pdb=" O SER A 79 " pdb=" OG1 THR A 82 " model vdw 2.262 3.040 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.266 3.120 nonbonded pdb=" OG SER A 125 " pdb=" OE2 GLU A 161 " model vdw 2.285 3.040 ... (remaining 48531 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: 5.580 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.900 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: 0.010 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 0.038 6011 Z= 0.211 Angle : 0.882 9.623 8188 Z= 0.477 Chirality : 0.057 0.363 924 Planarity : 0.007 0.110 1043 Dihedral : 16.254 87.225 2133 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 0.61 % Allowed : 27.09 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.99 (0.32), residues: 711 helix: 0.74 (0.67), residues: 54 sheet: 1.01 (0.29), residues: 305 loop : 0.46 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 41 TYR 0.016 0.002 TYR L 49 PHE 0.032 0.002 PHE A 115 TRP 0.013 0.001 TRP B 131 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.21 ( 6004) covalent geometry : angle 0.88270 / 0.48 ( 8174) SS BOND : bond 0.00255 / 0.15 ( 7) SS BOND : angle 0.52402 / 0.24 ( 14) hydrogen bonds : bond 0.12577 / 9.05 ( 255) hydrogen bonds : angle 6.34410 / 4.45 ( 717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.147 Fit side-chains REVERT: H 73 ASP cc_start: 0.8128 (t0) cc_final: 0.7285 (p0) REVERT: L 17 ASP cc_start: 0.8482 (t0) cc_final: 0.8141 (t0) REVERT: L 50 ASP cc_start: 0.8703 (t0) cc_final: 0.8481 (t0) REVERT: L 78 LEU cc_start: 0.8952 (mp) cc_final: 0.8633 (mp) REVERT: L 140 PHE cc_start: 0.8404 (p90) cc_final: 0.8161 (p90) REVERT: B 70 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7850 (ptm-80) REVERT: B 152 ASP cc_start: 0.8989 (t0) cc_final: 0.8560 (t0) outliers start: 4 outliers final: 2 residues processed: 150 average time/residue: 0.3891 time to fit residues: 61.3317 Evaluate side-chains 139 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN A 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078563 restraints weight = 11471.882| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.49 r_work: 0.2979 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6011 Z= 0.139 Angle : 0.658 8.205 8188 Z= 0.328 Chirality : 0.046 0.188 924 Planarity : 0.006 0.096 1043 Dihedral : 5.261 58.611 804 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.11 % Favored : 97.75 % Rotamer: Outliers : 3.81 % Allowed : 23.74 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.09 (0.32), residues: 711 helix: 1.22 (0.68), residues: 54 sheet: 1.17 (0.29), residues: 304 loop : 0.34 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.014 0.001 TYR A 11 PHE 0.016 0.001 PHE L 117 TRP 0.008 0.001 TRP H 112 HIS 0.002 0.000 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6004) covalent geometry : angle 0.65872 / 0.33 ( 8174) SS BOND : bond 0.00233 / 0.13 ( 7) SS BOND : angle 0.40229 / 0.20 ( 14) hydrogen bonds : bond 0.03596 / 2.44 ( 255) hydrogen bonds : angle 5.47937 / 3.82 ( 717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.148 Fit side-chains REVERT: H 43 LYS cc_start: 0.8935 (mppt) cc_final: 0.8613 (mppt) REVERT: H 89 GLU cc_start: 0.9068 (pm20) cc_final: 0.8854 (pm20) REVERT: L 17 ASP cc_start: 0.8523 (t0) cc_final: 0.8030 (t0) REVERT: L 30 SER cc_start: 0.8502 (m) cc_final: 0.8021 (t) REVERT: L 50 ASP cc_start: 0.8707 (t0) cc_final: 0.8435 (t0) REVERT: L 78 LEU cc_start: 0.8826 (mp) cc_final: 0.8479 (mp) REVERT: L 108 LYS cc_start: 0.7962 (tptm) cc_final: 0.7576 (mmmt) REVERT: L 166 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8641 (mm-30) REVERT: B 25 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7699 (ttp80) REVERT: B 114 LEU cc_start: 0.9204 (pp) cc_final: 0.8766 (tp) REVERT: B 152 ASP cc_start: 0.9008 (t0) cc_final: 0.8528 (t0) outliers start: 25 outliers final: 9 residues processed: 168 average time/residue: 0.3957 time to fit residues: 69.9253 Evaluate side-chains 145 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.110507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077946 restraints weight = 11204.443| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.48 r_work: 0.2970 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6011 Z= 0.145 Angle : 0.645 7.909 8188 Z= 0.322 Chirality : 0.045 0.175 924 Planarity : 0.006 0.093 1043 Dihedral : 5.722 70.539 804 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer: Outliers : 3.96 % Allowed : 24.35 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.15 (0.32), residues: 711 helix: 1.55 (0.70), residues: 54 sheet: 1.18 (0.28), residues: 314 loop : 0.33 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 41 TYR 0.014 0.001 TYR A 11 PHE 0.015 0.001 PHE A 148 TRP 0.008 0.001 TRP H 112 HIS 0.002 0.000 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6004) covalent geometry : angle 0.64492 / 0.32 ( 8174) SS BOND : bond 0.00255 / 0.16 ( 7) SS BOND : angle 0.54025 / 0.29 ( 14) hydrogen bonds : bond 0.03352 / 2.27 ( 255) hydrogen bonds : angle 5.25253 / 3.66 ( 717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.177 Fit side-chains REVERT: H 43 LYS cc_start: 0.9004 (mppt) cc_final: 0.8639 (mppt) REVERT: H 89 GLU cc_start: 0.9091 (pm20) cc_final: 0.8789 (pm20) REVERT: H 218 LYS cc_start: 0.7397 (tptt) cc_final: 0.6815 (tttm) REVERT: L 17 ASP cc_start: 0.8548 (t0) cc_final: 0.8278 (t0) REVERT: L 30 SER cc_start: 0.8466 (m) cc_final: 0.7951 (t) REVERT: L 50 ASP cc_start: 0.8730 (t0) cc_final: 0.8395 (t0) REVERT: L 70 GLU cc_start: 0.8035 (tp30) cc_final: 0.7811 (tp30) REVERT: L 108 LYS cc_start: 0.8010 (tptm) cc_final: 0.7613 (mmmt) REVERT: B 25 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: B 114 LEU cc_start: 0.9174 (pp) cc_final: 0.8804 (tp) REVERT: B 152 ASP cc_start: 0.9009 (t0) cc_final: 0.8562 (t0) REVERT: A 55 ARG cc_start: 0.8322 (mtm110) cc_final: 0.8076 (mtm-85) outliers start: 26 outliers final: 14 residues processed: 164 average time/residue: 0.4120 time to fit residues: 71.0583 Evaluate side-chains 150 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.076472 restraints weight = 11491.657| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.53 r_work: 0.2948 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6011 Z= 0.163 Angle : 0.657 7.790 8188 Z= 0.329 Chirality : 0.045 0.175 924 Planarity : 0.006 0.090 1043 Dihedral : 5.634 66.854 804 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.25 % Favored : 97.61 % Rotamer: Outliers : 3.81 % Allowed : 25.27 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.32), residues: 711 helix: 1.68 (0.71), residues: 54 sheet: 1.10 (0.28), residues: 324 loop : 0.31 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 41 TYR 0.016 0.002 TYR A 11 PHE 0.018 0.002 PHE L 117 TRP 0.009 0.001 TRP H 112 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 6004) covalent geometry : angle 0.65750 / 0.33 ( 8174) SS BOND : bond 0.00323 / 0.19 ( 7) SS BOND : angle 0.51945 / 0.28 ( 14) hydrogen bonds : bond 0.03432 / 2.31 ( 255) hydrogen bonds : angle 5.19405 / 3.63 ( 717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.166 Fit side-chains REVERT: H 43 LYS cc_start: 0.9077 (mppt) cc_final: 0.8637 (mppt) REVERT: H 89 GLU cc_start: 0.9124 (pm20) cc_final: 0.8720 (pm20) REVERT: H 104 GLU cc_start: 0.9026 (mp0) cc_final: 0.8744 (mp0) REVERT: H 154 TYR cc_start: 0.7180 (p90) cc_final: 0.6539 (p90) REVERT: H 218 LYS cc_start: 0.7392 (tptt) cc_final: 0.6819 (tttm) REVERT: L 17 ASP cc_start: 0.8558 (t0) cc_final: 0.8302 (t0) REVERT: L 50 ASP cc_start: 0.8738 (t0) cc_final: 0.8487 (t0) REVERT: B 25 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7996 (ttp80) REVERT: B 114 LEU cc_start: 0.9172 (pp) cc_final: 0.8838 (tp) REVERT: B 152 ASP cc_start: 0.9017 (t0) cc_final: 0.8571 (t0) REVERT: A 55 ARG cc_start: 0.8303 (mtm110) cc_final: 0.7919 (mtm-85) outliers start: 25 outliers final: 12 residues processed: 161 average time/residue: 0.4101 time to fit residues: 69.5958 Evaluate side-chains 147 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 0.0030 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073185 restraints weight = 11582.272| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.47 r_work: 0.2885 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 6011 Z= 0.262 Angle : 0.722 7.989 8188 Z= 0.365 Chirality : 0.047 0.176 924 Planarity : 0.006 0.089 1043 Dihedral : 5.597 64.500 803 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 5.48 % Allowed : 25.11 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.01 (0.32), residues: 711 helix: 1.47 (0.71), residues: 54 sheet: 1.08 (0.29), residues: 310 loop : 0.25 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 41 TYR 0.018 0.002 TYR A 11 PHE 0.022 0.002 PHE H 155 TRP 0.011 0.001 TRP H 112 HIS 0.007 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 ( 6004) covalent geometry : angle 0.72220 / 0.37 ( 8174) SS BOND : bond 0.00463 / 0.30 ( 7) SS BOND : angle 0.79919 / 0.44 ( 14) hydrogen bonds : bond 0.03888 / 2.63 ( 255) hydrogen bonds : angle 5.35233 / 3.74 ( 717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.9104 (mppt) cc_final: 0.8612 (mppt) REVERT: H 89 GLU cc_start: 0.9144 (pm20) cc_final: 0.8729 (pm20) REVERT: H 104 GLU cc_start: 0.9068 (mp0) cc_final: 0.8806 (mp0) REVERT: H 218 LYS cc_start: 0.7478 (tptt) cc_final: 0.6875 (tttm) REVERT: L 17 ASP cc_start: 0.8546 (t0) cc_final: 0.8292 (t0) REVERT: L 50 ASP cc_start: 0.8766 (t0) cc_final: 0.8495 (t0) REVERT: B 25 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7906 (ttp80) REVERT: B 114 LEU cc_start: 0.9205 (pp) cc_final: 0.8923 (tp) REVERT: B 133 ARG cc_start: 0.8806 (ttt180) cc_final: 0.8379 (tpp-160) REVERT: B 152 ASP cc_start: 0.9109 (t0) cc_final: 0.8601 (t0) REVERT: A 55 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7871 (mtm-85) outliers start: 36 outliers final: 18 residues processed: 159 average time/residue: 0.4119 time to fit residues: 69.0761 Evaluate side-chains 147 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN A 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077119 restraints weight = 11471.153| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.51 r_work: 0.2952 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6011 Z= 0.145 Angle : 0.682 9.490 8188 Z= 0.339 Chirality : 0.046 0.176 924 Planarity : 0.006 0.084 1043 Dihedral : 5.595 73.929 803 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Rotamer: Outliers : 3.96 % Allowed : 27.25 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.11 (0.32), residues: 711 helix: 1.73 (0.73), residues: 54 sheet: 1.14 (0.29), residues: 320 loop : 0.27 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 41 TYR 0.014 0.001 TYR A 11 PHE 0.020 0.002 PHE L 117 TRP 0.009 0.001 TRP B 131 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 6004) covalent geometry : angle 0.68254 / 0.34 ( 8174) SS BOND : bond 0.00169 / 0.11 ( 7) SS BOND : angle 0.44814 / 0.25 ( 14) hydrogen bonds : bond 0.03320 / 2.24 ( 255) hydrogen bonds : angle 5.08854 / 3.55 ( 717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.158 Fit side-chains REVERT: H 43 LYS cc_start: 0.9112 (mppt) cc_final: 0.8588 (mppt) REVERT: H 89 GLU cc_start: 0.9133 (pm20) cc_final: 0.8785 (pm20) REVERT: H 104 GLU cc_start: 0.9020 (mp0) cc_final: 0.8772 (mp0) REVERT: H 154 TYR cc_start: 0.7223 (p90) cc_final: 0.6286 (p90) REVERT: H 218 LYS cc_start: 0.7449 (tptt) cc_final: 0.6733 (tttm) REVERT: L 17 ASP cc_start: 0.8562 (t0) cc_final: 0.8349 (t0) REVERT: L 50 ASP cc_start: 0.8684 (t0) cc_final: 0.8418 (t0) REVERT: B 25 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7979 (ttp80) REVERT: B 70 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.7762 (ptm-80) REVERT: B 114 LEU cc_start: 0.9189 (pp) cc_final: 0.8934 (tp) REVERT: B 128 LYS cc_start: 0.8743 (tptp) cc_final: 0.8499 (tptt) REVERT: B 133 ARG cc_start: 0.8798 (ttt180) cc_final: 0.8341 (tpp-160) REVERT: B 152 ASP cc_start: 0.9032 (t0) cc_final: 0.8560 (t0) REVERT: A 55 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7949 (mtm-85) REVERT: A 115 PHE cc_start: 0.7775 (t80) cc_final: 0.7564 (t80) outliers start: 26 outliers final: 12 residues processed: 160 average time/residue: 0.3930 time to fit residues: 66.2452 Evaluate side-chains 144 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.109498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076949 restraints weight = 11372.239| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.51 r_work: 0.2949 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6011 Z= 0.156 Angle : 0.696 8.556 8188 Z= 0.347 Chirality : 0.046 0.201 924 Planarity : 0.006 0.082 1043 Dihedral : 5.549 70.571 803 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 4.87 % Allowed : 26.79 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.13 (0.32), residues: 711 helix: 1.52 (0.73), residues: 54 sheet: 1.22 (0.29), residues: 320 loop : 0.24 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 41 TYR 0.031 0.002 TYR H 154 PHE 0.014 0.001 PHE A 148 TRP 0.008 0.001 TRP H 112 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6004) covalent geometry : angle 0.69673 / 0.35 ( 8174) SS BOND : bond 0.00221 / 0.14 ( 7) SS BOND : angle 0.49563 / 0.28 ( 14) hydrogen bonds : bond 0.03325 / 2.26 ( 255) hydrogen bonds : angle 4.98197 / 3.49 ( 717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.203 Fit side-chains REVERT: H 43 LYS cc_start: 0.9131 (mppt) cc_final: 0.8603 (mppt) REVERT: H 89 GLU cc_start: 0.9124 (pm20) cc_final: 0.8803 (pm20) REVERT: H 104 GLU cc_start: 0.9027 (mp0) cc_final: 0.8775 (mp0) REVERT: H 218 LYS cc_start: 0.7466 (tptt) cc_final: 0.6783 (tttm) REVERT: L 50 ASP cc_start: 0.8699 (t0) cc_final: 0.8400 (t0) REVERT: L 108 LYS cc_start: 0.8191 (tptm) cc_final: 0.7913 (mtpp) REVERT: B 25 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8018 (ttp80) REVERT: B 114 LEU cc_start: 0.9182 (pp) cc_final: 0.8951 (tp) REVERT: B 128 LYS cc_start: 0.8713 (tptp) cc_final: 0.8443 (tptt) REVERT: B 133 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8338 (tpp-160) REVERT: B 152 ASP cc_start: 0.9038 (t0) cc_final: 0.8571 (t0) REVERT: A 55 ARG cc_start: 0.8213 (mtm110) cc_final: 0.8012 (mtm180) REVERT: A 166 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8472 (tptm) outliers start: 32 outliers final: 15 residues processed: 164 average time/residue: 0.3613 time to fit residues: 62.4225 Evaluate side-chains 149 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076077 restraints weight = 11356.102| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.48 r_work: 0.2933 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6011 Z= 0.183 Angle : 0.727 8.766 8188 Z= 0.363 Chirality : 0.047 0.205 924 Planarity : 0.006 0.080 1043 Dihedral : 5.616 70.588 803 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 3.81 % Allowed : 28.01 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.10 (0.32), residues: 711 helix: 1.52 (0.74), residues: 54 sheet: 1.15 (0.29), residues: 324 loop : 0.26 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 41 TYR 0.031 0.002 TYR H 154 PHE 0.020 0.002 PHE L 117 TRP 0.008 0.001 TRP H 112 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 6004) covalent geometry : angle 0.72710 / 0.36 ( 8174) SS BOND : bond 0.00283 / 0.18 ( 7) SS BOND : angle 0.58430 / 0.32 ( 14) hydrogen bonds : bond 0.03429 / 2.33 ( 255) hydrogen bonds : angle 5.05089 / 3.54 ( 717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.230 Fit side-chains REVERT: H 43 LYS cc_start: 0.9126 (mppt) cc_final: 0.8611 (mppt) REVERT: H 89 GLU cc_start: 0.9131 (pm20) cc_final: 0.8803 (pm20) REVERT: H 104 GLU cc_start: 0.9043 (mp0) cc_final: 0.8800 (mp0) REVERT: H 154 TYR cc_start: 0.7545 (p90) cc_final: 0.7030 (p90) REVERT: H 218 LYS cc_start: 0.7561 (tptt) cc_final: 0.6857 (tttp) REVERT: L 17 ASP cc_start: 0.8397 (t70) cc_final: 0.8148 (t0) REVERT: L 24 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7564 (tpp80) REVERT: L 50 ASP cc_start: 0.8716 (t0) cc_final: 0.8435 (t0) REVERT: L 78 LEU cc_start: 0.8893 (mp) cc_final: 0.8544 (mp) REVERT: L 108 LYS cc_start: 0.8213 (tptm) cc_final: 0.7944 (mtpp) REVERT: B 25 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8029 (ttp80) REVERT: B 70 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7802 (ptm-80) REVERT: B 114 LEU cc_start: 0.9215 (pp) cc_final: 0.8979 (tp) REVERT: B 128 LYS cc_start: 0.8728 (tptp) cc_final: 0.8440 (tptt) REVERT: B 133 ARG cc_start: 0.8773 (ttt180) cc_final: 0.8338 (tpp-160) REVERT: B 152 ASP cc_start: 0.9055 (t0) cc_final: 0.8590 (t0) REVERT: A 53 ARG cc_start: 0.7925 (tpt170) cc_final: 0.7586 (tpm170) REVERT: A 55 ARG cc_start: 0.8210 (mtm110) cc_final: 0.7799 (mtm110) REVERT: A 166 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8459 (tptm) outliers start: 25 outliers final: 13 residues processed: 155 average time/residue: 0.4308 time to fit residues: 70.1794 Evaluate side-chains 148 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.109864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077534 restraints weight = 11388.397| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.52 r_work: 0.2961 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6011 Z= 0.155 Angle : 0.735 8.740 8188 Z= 0.366 Chirality : 0.047 0.220 924 Planarity : 0.006 0.079 1043 Dihedral : 5.487 64.770 803 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 3.65 % Allowed : 28.92 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.32), residues: 711 helix: 1.39 (0.75), residues: 53 sheet: 1.20 (0.29), residues: 320 loop : 0.21 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 41 TYR 0.032 0.002 TYR L 49 PHE 0.025 0.002 PHE L 140 TRP 0.008 0.001 TRP B 131 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6004) covalent geometry : angle 0.73588 / 0.37 ( 8174) SS BOND : bond 0.00202 / 0.13 ( 7) SS BOND : angle 0.41739 / 0.23 ( 14) hydrogen bonds : bond 0.03244 / 2.20 ( 255) hydrogen bonds : angle 4.96954 / 3.48 ( 717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.150 Fit side-chains REVERT: H 43 LYS cc_start: 0.9178 (mppt) cc_final: 0.8648 (mppt) REVERT: H 89 GLU cc_start: 0.9112 (pm20) cc_final: 0.8780 (pm20) REVERT: H 104 GLU cc_start: 0.9030 (mp0) cc_final: 0.8812 (mp0) REVERT: H 154 TYR cc_start: 0.7635 (p90) cc_final: 0.7112 (p90) REVERT: H 218 LYS cc_start: 0.7650 (tptt) cc_final: 0.6926 (tttp) REVERT: L 4 MET cc_start: 0.9200 (mmm) cc_final: 0.8927 (tpt) REVERT: L 17 ASP cc_start: 0.8468 (t70) cc_final: 0.8232 (t0) REVERT: L 24 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7300 (tpp80) REVERT: L 50 ASP cc_start: 0.8661 (t0) cc_final: 0.8384 (t0) REVERT: L 78 LEU cc_start: 0.8923 (mp) cc_final: 0.8555 (mp) REVERT: L 108 LYS cc_start: 0.8182 (tptm) cc_final: 0.7921 (mtpp) REVERT: B 25 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8038 (ttp80) REVERT: B 114 LEU cc_start: 0.9198 (pp) cc_final: 0.8992 (tp) REVERT: B 133 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8307 (tpp-160) REVERT: B 152 ASP cc_start: 0.9034 (t0) cc_final: 0.8582 (OUTLIER) REVERT: A 53 ARG cc_start: 0.7943 (tpt170) cc_final: 0.7724 (tpm170) REVERT: A 166 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8454 (tptm) outliers start: 24 outliers final: 13 residues processed: 162 average time/residue: 0.3844 time to fit residues: 65.2617 Evaluate side-chains 150 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 0.0000 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.0050 chunk 10 optimal weight: 0.0030 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 57 ASN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081754 restraints weight = 11484.200| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.61 r_work: 0.3042 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6011 Z= 0.133 Angle : 0.741 9.417 8188 Z= 0.369 Chirality : 0.047 0.221 924 Planarity : 0.006 0.087 1043 Dihedral : 5.225 55.470 803 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.95 % Favored : 96.91 % Rotamer: Outliers : 1.98 % Allowed : 31.05 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.14 (0.32), residues: 711 helix: 0.99 (0.70), residues: 54 sheet: 1.33 (0.29), residues: 320 loop : 0.23 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 41 TYR 0.030 0.002 TYR L 49 PHE 0.017 0.001 PHE L 117 TRP 0.011 0.001 TRP B 131 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 6004) covalent geometry : angle 0.74129 / 0.37 ( 8174) SS BOND : bond 0.00177 / 0.08 ( 7) SS BOND : angle 0.37493 / 0.21 ( 14) hydrogen bonds : bond 0.03093 / 2.11 ( 255) hydrogen bonds : angle 4.81845 / 3.37 ( 717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.176 Fit side-chains REVERT: H 43 LYS cc_start: 0.9212 (mppt) cc_final: 0.8688 (mppt) REVERT: H 57 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8513 (m110) REVERT: H 89 GLU cc_start: 0.9113 (pm20) cc_final: 0.8784 (pm20) REVERT: H 104 GLU cc_start: 0.9001 (mp0) cc_final: 0.8782 (mp0) REVERT: H 154 TYR cc_start: 0.7654 (p90) cc_final: 0.6978 (p90) REVERT: H 218 LYS cc_start: 0.7654 (tptt) cc_final: 0.6987 (tttp) REVERT: L 4 MET cc_start: 0.9192 (mmm) cc_final: 0.8942 (tpt) REVERT: L 17 ASP cc_start: 0.8564 (t70) cc_final: 0.8356 (t0) REVERT: L 24 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7317 (tpp80) REVERT: L 50 ASP cc_start: 0.8587 (t0) cc_final: 0.8295 (t0) REVERT: L 78 LEU cc_start: 0.8941 (mp) cc_final: 0.8680 (mp) REVERT: L 108 LYS cc_start: 0.8133 (tptm) cc_final: 0.7750 (mmmt) REVERT: B 133 ARG cc_start: 0.8740 (ttt180) cc_final: 0.8281 (tpp-160) REVERT: B 152 ASP cc_start: 0.8974 (t0) cc_final: 0.8569 (OUTLIER) REVERT: B 174 HIS cc_start: 0.7893 (m170) cc_final: 0.7687 (m170) REVERT: A 53 ARG cc_start: 0.7946 (tpt170) cc_final: 0.7735 (tpm170) REVERT: A 55 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7885 (mtt90) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 0.3930 time to fit residues: 64.8767 Evaluate side-chains 145 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 173 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 57 ASN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 82 ASN A 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.111739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079536 restraints weight = 11386.840| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.55 r_work: 0.3001 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6011 Z= 0.153 Angle : 0.750 9.651 8188 Z= 0.377 Chirality : 0.047 0.213 924 Planarity : 0.006 0.073 1043 Dihedral : 5.756 87.601 803 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.67 % Favored : 97.19 % Rotamer: Outliers : 2.74 % Allowed : 29.68 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.18 (0.32), residues: 711 helix: 1.11 (0.71), residues: 54 sheet: 1.35 (0.29), residues: 320 loop : 0.25 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 41 TYR 0.031 0.002 TYR L 49 PHE 0.025 0.002 PHE L 140 TRP 0.010 0.001 TRP B 131 HIS 0.002 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 6004) covalent geometry : angle 0.75082 / 0.38 ( 8174) SS BOND : bond 0.00180 / 0.11 ( 7) SS BOND : angle 0.38112 / 0.21 ( 14) hydrogen bonds : bond 0.03241 / 2.23 ( 255) hydrogen bonds : angle 4.83667 / 3.39 ( 717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.33 seconds wall clock time: 37 minutes 2.29 seconds (2222.29 seconds total)