Starting phenix.real_space_refine on Thu Jul 2 00:39:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpg_26054/07_2026/7tpg_26054.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpg_26054/07_2026/7tpg_26054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tpg_26054/07_2026/7tpg_26054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpg_26054/07_2026/7tpg_26054.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tpg_26054/07_2026/7tpg_26054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpg_26054/07_2026/7tpg_26054.map" } resolution = 3.23 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 32 5.16 5 C 3081 2.51 5 N 816 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4777 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3053 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'GPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.90, per 1000 atoms: 0.19 Number of scatterers: 4777 At special positions: 0 Unit cell: (76.392, 77.453, 107.161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 2 15.00 O 846 8.00 N 816 7.00 C 3081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 0.35 Conformation dependent library (CDL) restraints added in 141.9 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 54.5% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.525A pdb=" N LEU B 15 " --> pdb=" O MET B 11 " (cutoff:3.500A) Proline residue: B 20 - end of helix Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 58 through 79 removed outlier: 3.661A pdb=" N LEU B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.626A pdb=" N ASP B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 106 removed outlier: 3.597A pdb=" N LEU B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.019A pdb=" N TRP B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 162 removed outlier: 3.533A pdb=" N ALA B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 188 removed outlier: 3.668A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.788A pdb=" N VAL B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.535A pdb=" N TYR B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.857A pdb=" N ASP B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.568A pdb=" N TRP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 removed outlier: 4.297A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 302 removed outlier: 3.563A pdb=" N HIS B 300 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 314 through 353 removed outlier: 7.760A pdb=" N ILE B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Proline residue: B 326 - end of helix removed outlier: 3.813A pdb=" N PHE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.533A pdb=" N VAL B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 382 removed outlier: 3.504A pdb=" N ALA B 382 " --> pdb=" O VAL B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 383 through 407 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.769A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.584A pdb=" N TYR H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 100 through 102 removed outlier: 6.792A pdb=" N ARG H 101 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.552A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.552A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 810 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: 0.57 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1508 1.35 - 1.46: 1231 1.46 - 1.58: 2091 1.58 - 1.70: 3 1.70 - 1.82: 55 Bond restraints: 4888 Sorted by residual: bond pdb=" O3A GPP H 301 " pdb=" PA GPP H 301 " ideal model delta sigma weight residual 1.589 1.648 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C6 GPP H 301 " pdb=" C7 GPP H 301 " ideal model delta sigma weight residual 1.499 1.545 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C3 GPP H 301 " pdb=" C5 GPP H 301 " ideal model delta sigma weight residual 1.509 1.554 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" O3A GPP H 301 " pdb=" PB GPP H 301 " ideal model delta sigma weight residual 1.702 1.657 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" C1 GPP H 301 " pdb=" C2 GPP H 301 " ideal model delta sigma weight residual 1.496 1.540 -0.044 2.00e-02 2.50e+03 4.78e+00 ... (remaining 4883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 6574 2.54 - 5.09: 60 5.09 - 7.63: 9 7.63 - 10.18: 5 10.18 - 12.72: 2 Bond angle restraints: 6650 Sorted by residual: angle pdb=" C HIS B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta sigma weight residual 122.74 134.31 -11.57 2.44e+00 1.68e-01 2.25e+01 angle pdb=" PA GPP H 301 " pdb=" O3A GPP H 301 " pdb=" PB GPP H 301 " ideal model delta sigma weight residual 136.52 123.80 12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N ARG B 211 " pdb=" CA ARG B 211 " pdb=" C ARG B 211 " ideal model delta sigma weight residual 114.64 109.04 5.60 1.52e+00 4.33e-01 1.36e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N LEU B 205 " pdb=" CA LEU B 205 " pdb=" C LEU B 205 " ideal model delta sigma weight residual 113.20 109.43 3.77 1.21e+00 6.83e-01 9.71e+00 ... (remaining 6645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2604 17.88 - 35.76: 194 35.76 - 53.63: 51 53.63 - 71.51: 6 71.51 - 89.39: 6 Dihedral angle restraints: 2861 sinusoidal: 1074 harmonic: 1787 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 146.21 -53.21 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA GLN B 255 " pdb=" C GLN B 255 " pdb=" N GLY B 256 " pdb=" CA GLY B 256 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG B 254 " pdb=" C ARG B 254 " pdb=" N GLN B 255 " pdb=" CA GLN B 255 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 464 0.030 - 0.060: 210 0.060 - 0.090: 55 0.090 - 0.120: 28 0.120 - 0.150: 6 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA ASP H 114 " pdb=" N ASP H 114 " pdb=" C ASP H 114 " pdb=" CB ASP H 114 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA THR B 60 " pdb=" N THR B 60 " pdb=" C THR B 60 " pdb=" CB THR B 60 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB THR B 323 " pdb=" CA THR B 323 " pdb=" OG1 THR B 323 " pdb=" CG2 THR B 323 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 760 not shown) Planarity restraints: 826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 101 " -0.022 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP B 101 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 101 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 101 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 89 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 90 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 107 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 108 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.018 5.00e-02 4.00e+02 ... (remaining 823 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 38 2.64 - 3.21: 4380 3.21 - 3.77: 7273 3.77 - 4.34: 9748 4.34 - 4.90: 16638 Nonbonded interactions: 38077 Sorted by model distance: nonbonded pdb=" O SER B 56 " pdb=" OG1 THR B 60 " model vdw 2.078 3.040 nonbonded pdb=" OG SER H 55 " pdb=" OG SER H 60 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASP H 114 " pdb=" N TYR H 115 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASP B 166 " pdb=" NH1 ARG B 211 " model vdw 2.315 3.120 nonbonded pdb=" NH1 ARG L 62 " pdb=" OD2 ASP L 83 " model vdw 2.331 3.120 ... (remaining 38072 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.290 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.003 0.059 4891 Z= 0.159 Angle : 0.704 12.719 6656 Z= 0.368 Chirality : 0.040 0.150 763 Planarity : 0.004 0.039 826 Dihedral : 14.172 89.388 1714 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.79 (0.35), residues: 620 helix: 1.46 (0.30), residues: 310 sheet: 0.49 (0.57), residues: 87 loop : -0.76 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 50 TYR 0.015 0.001 TYR H 115 PHE 0.018 0.001 PHE L 72 TRP 0.044 0.001 TRP B 101 HIS 0.002 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 ( 4888) covalent geometry : angle 0.70359 / 0.37 ( 6650) SS BOND : bond 0.00262 / 0.13 ( 3) SS BOND : angle 0.95531 / 0.56 ( 6) hydrogen bonds : bond 0.18007 / 11.31 ( 279) hydrogen bonds : angle 7.08565 / 4.90 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.110 Fit side-chains REVERT: B 34 LEU cc_start: 0.6880 (tp) cc_final: 0.6473 (tp) REVERT: B 50 ARG cc_start: 0.6447 (mtm-85) cc_final: 0.5867 (mtm-85) REVERT: B 143 TRP cc_start: 0.8336 (m100) cc_final: 0.8084 (m-90) REVERT: B 191 ARG cc_start: 0.7140 (tmt170) cc_final: 0.6816 (tpt170) REVERT: B 216 MET cc_start: 0.5599 (mtt) cc_final: 0.5068 (mtt) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.0557 time to fit residues: 7.4999 Evaluate side-chains 89 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 ASN B 274 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128256 restraints weight = 5757.372| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.46 r_work: 0.3245 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4891 Z= 0.116 Angle : 0.548 6.847 6656 Z= 0.287 Chirality : 0.041 0.138 763 Planarity : 0.004 0.034 826 Dihedral : 6.311 57.168 699 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.20 % Allowed : 8.22 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.80 (0.34), residues: 620 helix: 1.72 (0.30), residues: 311 sheet: 0.20 (0.54), residues: 96 loop : -1.08 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.009 0.001 TYR B 275 PHE 0.013 0.001 PHE L 72 TRP 0.035 0.001 TRP B 101 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 4888) covalent geometry : angle 0.54654 / 0.29 ( 6650) SS BOND : bond 0.00439 / 0.22 ( 3) SS BOND : angle 1.35232 / 0.85 ( 6) hydrogen bonds : bond 0.03734 / 2.48 ( 279) hydrogen bonds : angle 4.59841 / 3.26 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: B 34 LEU cc_start: 0.6643 (tp) cc_final: 0.6003 (mp) REVERT: B 50 ARG cc_start: 0.6807 (mtm-85) cc_final: 0.5988 (mtm-85) REVERT: B 191 ARG cc_start: 0.7305 (tmt170) cc_final: 0.6375 (tpt170) REVERT: H 86 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8158 (mtp) outliers start: 6 outliers final: 4 residues processed: 93 average time/residue: 0.0679 time to fit residues: 7.9401 Evaluate side-chains 87 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 53 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 42 optimal weight: 0.9980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN B 251 GLN B 354 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110423 restraints weight = 6218.153| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.68 r_work: 0.3144 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4891 Z= 0.150 Angle : 0.557 5.954 6656 Z= 0.291 Chirality : 0.042 0.151 763 Planarity : 0.004 0.037 826 Dihedral : 6.342 57.764 697 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.60 % Allowed : 11.42 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.76 (0.34), residues: 620 helix: 1.65 (0.30), residues: 317 sheet: 0.76 (0.59), residues: 79 loop : -1.29 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.009 0.001 TYR H 53 PHE 0.010 0.001 PHE B 212 TRP 0.032 0.001 TRP B 101 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 4888) covalent geometry : angle 0.55513 / 0.29 ( 6650) SS BOND : bond 0.00536 / 0.27 ( 3) SS BOND : angle 1.49840 / 1.02 ( 6) hydrogen bonds : bond 0.03731 / 2.48 ( 279) hydrogen bonds : angle 4.28432 / 3.05 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.119 Fit side-chains REVERT: B 34 LEU cc_start: 0.6944 (tp) cc_final: 0.6332 (mp) REVERT: B 79 TYR cc_start: 0.8368 (t80) cc_final: 0.8037 (t80) REVERT: B 191 ARG cc_start: 0.7296 (tmt170) cc_final: 0.6345 (tpt170) REVERT: B 232 TYR cc_start: 0.6757 (t80) cc_final: 0.6213 (t80) REVERT: H 86 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8518 (mtp) outliers start: 8 outliers final: 3 residues processed: 94 average time/residue: 0.0696 time to fit residues: 8.2200 Evaluate side-chains 88 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109833 restraints weight = 6214.824| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.68 r_work: 0.3139 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4891 Z= 0.142 Angle : 0.541 6.080 6656 Z= 0.285 Chirality : 0.042 0.146 763 Planarity : 0.004 0.040 826 Dihedral : 6.193 57.787 697 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.40 % Allowed : 12.63 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.80 (0.34), residues: 620 helix: 1.66 (0.30), residues: 317 sheet: 0.82 (0.60), residues: 79 loop : -1.26 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.010 0.001 TYR H 53 PHE 0.011 0.001 PHE B 212 TRP 0.029 0.001 TRP B 101 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4888) covalent geometry : angle 0.53985 / 0.28 ( 6650) SS BOND : bond 0.00516 / 0.26 ( 3) SS BOND : angle 1.43649 / 0.95 ( 6) hydrogen bonds : bond 0.03497 / 2.35 ( 279) hydrogen bonds : angle 4.12278 / 2.94 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.166 Fit side-chains REVERT: B 79 TYR cc_start: 0.8361 (t80) cc_final: 0.8109 (t80) REVERT: B 168 ARG cc_start: 0.6511 (ttp80) cc_final: 0.6065 (ttm-80) REVERT: B 232 TYR cc_start: 0.6656 (t80) cc_final: 0.6318 (t80) REVERT: B 331 MET cc_start: 0.8481 (tmm) cc_final: 0.8259 (tmm) REVERT: L 82 GLU cc_start: 0.8389 (pm20) cc_final: 0.8162 (pm20) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.0687 time to fit residues: 8.1770 Evaluate side-chains 87 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111331 restraints weight = 6180.419| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.68 r_work: 0.3146 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4891 Z= 0.125 Angle : 0.518 6.121 6656 Z= 0.273 Chirality : 0.041 0.155 763 Planarity : 0.004 0.036 826 Dihedral : 5.966 56.806 697 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.00 % Allowed : 16.03 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.85 (0.34), residues: 620 helix: 1.69 (0.30), residues: 318 sheet: 0.81 (0.60), residues: 79 loop : -1.22 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.010 0.001 TYR H 53 PHE 0.016 0.001 PHE B 212 TRP 0.027 0.001 TRP B 101 HIS 0.004 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 4888) covalent geometry : angle 0.51691 / 0.27 ( 6650) SS BOND : bond 0.00469 / 0.24 ( 3) SS BOND : angle 1.33564 / 0.86 ( 6) hydrogen bonds : bond 0.03272 / 2.21 ( 279) hydrogen bonds : angle 3.97409 / 2.82 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.136 Fit side-chains REVERT: B 48 MET cc_start: 0.7196 (mmm) cc_final: 0.6881 (mmm) REVERT: B 168 ARG cc_start: 0.6451 (ttp80) cc_final: 0.5990 (ttm-80) REVERT: B 232 TYR cc_start: 0.6641 (t80) cc_final: 0.6310 (t80) REVERT: B 381 MET cc_start: 0.9074 (tpp) cc_final: 0.8850 (mmt) REVERT: L 82 GLU cc_start: 0.8374 (pm20) cc_final: 0.8105 (pm20) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.0744 time to fit residues: 7.8647 Evaluate side-chains 81 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112100 restraints weight = 6244.963| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.73 r_work: 0.3166 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4891 Z= 0.109 Angle : 0.502 6.103 6656 Z= 0.263 Chirality : 0.041 0.155 763 Planarity : 0.004 0.039 826 Dihedral : 5.647 53.207 697 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.20 % Allowed : 16.63 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.88 (0.34), residues: 620 helix: 1.75 (0.30), residues: 317 sheet: 0.62 (0.58), residues: 83 loop : -1.20 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.013 0.001 TYR H 33 PHE 0.009 0.001 PHE L 72 TRP 0.023 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4888) covalent geometry : angle 0.50044 / 0.26 ( 6650) SS BOND : bond 0.00371 / 0.19 ( 3) SS BOND : angle 1.21103 / 0.77 ( 6) hydrogen bonds : bond 0.03056 / 2.04 ( 279) hydrogen bonds : angle 3.84643 / 2.73 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.171 Fit side-chains REVERT: B 48 MET cc_start: 0.7154 (mmm) cc_final: 0.6893 (mmm) REVERT: B 232 TYR cc_start: 0.6566 (t80) cc_final: 0.6260 (t80) REVERT: B 381 MET cc_start: 0.9083 (tpp) cc_final: 0.8842 (mmt) REVERT: L 82 GLU cc_start: 0.8361 (pm20) cc_final: 0.8134 (pm20) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.0693 time to fit residues: 7.5982 Evaluate side-chains 83 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 ASN B 177 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112634 restraints weight = 6182.154| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.72 r_work: 0.3171 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4891 Z= 0.110 Angle : 0.508 6.587 6656 Z= 0.263 Chirality : 0.041 0.159 763 Planarity : 0.004 0.035 826 Dihedral : 5.243 45.265 697 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.00 % Allowed : 17.03 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.94 (0.35), residues: 620 helix: 1.81 (0.30), residues: 317 sheet: 0.67 (0.59), residues: 83 loop : -1.20 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 208 TYR 0.012 0.001 TYR H 33 PHE 0.015 0.001 PHE B 212 TRP 0.022 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4888) covalent geometry : angle 0.50656 / 0.26 ( 6650) SS BOND : bond 0.00379 / 0.19 ( 3) SS BOND : angle 1.15317 / 0.74 ( 6) hydrogen bonds : bond 0.03010 / 2.01 ( 279) hydrogen bonds : angle 3.78899 / 2.69 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.123 Fit side-chains REVERT: B 48 MET cc_start: 0.7121 (mmm) cc_final: 0.6888 (mmm) REVERT: B 168 ARG cc_start: 0.6435 (ttp80) cc_final: 0.5995 (ttm-80) REVERT: B 232 TYR cc_start: 0.6505 (t80) cc_final: 0.6253 (t80) REVERT: H 6 GLN cc_start: 0.7011 (pp30) cc_final: 0.6769 (pp30) REVERT: L 82 GLU cc_start: 0.8340 (pm20) cc_final: 0.8138 (pm20) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.0717 time to fit residues: 7.5588 Evaluate side-chains 83 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111869 restraints weight = 6286.878| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.71 r_work: 0.3157 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4891 Z= 0.116 Angle : 0.524 6.975 6656 Z= 0.270 Chirality : 0.041 0.163 763 Planarity : 0.004 0.037 826 Dihedral : 4.922 35.749 697 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.80 % Allowed : 18.04 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.35), residues: 620 helix: 1.98 (0.30), residues: 311 sheet: 0.71 (0.60), residues: 83 loop : -1.27 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.012 0.001 TYR H 33 PHE 0.008 0.001 PHE L 72 TRP 0.022 0.001 TRP B 101 HIS 0.003 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4888) covalent geometry : angle 0.52307 / 0.27 ( 6650) SS BOND : bond 0.00402 / 0.20 ( 3) SS BOND : angle 1.18616 / 0.76 ( 6) hydrogen bonds : bond 0.03042 / 2.04 ( 279) hydrogen bonds : angle 3.77654 / 2.67 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.108 Fit side-chains REVERT: B 48 MET cc_start: 0.7155 (mmm) cc_final: 0.6900 (mmm) REVERT: B 168 ARG cc_start: 0.6428 (ttp80) cc_final: 0.6016 (ttm-80) REVERT: B 232 TYR cc_start: 0.6460 (t80) cc_final: 0.6229 (t80) REVERT: H 6 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6757 (pp30) REVERT: L 82 GLU cc_start: 0.8397 (pm20) cc_final: 0.8174 (pm20) outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 0.0631 time to fit residues: 6.8783 Evaluate side-chains 84 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112680 restraints weight = 6157.004| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.68 r_work: 0.3171 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4891 Z= 0.110 Angle : 0.519 7.222 6656 Z= 0.267 Chirality : 0.041 0.165 763 Planarity : 0.004 0.038 826 Dihedral : 4.744 30.517 697 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.60 % Allowed : 17.64 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.35), residues: 620 helix: 2.00 (0.30), residues: 311 sheet: 0.74 (0.60), residues: 83 loop : -1.31 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.011 0.001 TYR H 33 PHE 0.016 0.001 PHE B 212 TRP 0.021 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4888) covalent geometry : angle 0.51796 / 0.27 ( 6650) SS BOND : bond 0.00411 / 0.21 ( 3) SS BOND : angle 1.15984 / 0.74 ( 6) hydrogen bonds : bond 0.02995 / 2.00 ( 279) hydrogen bonds : angle 3.74979 / 2.65 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.150 Fit side-chains REVERT: B 48 MET cc_start: 0.7147 (mmm) cc_final: 0.6909 (mmm) REVERT: B 168 ARG cc_start: 0.6453 (ttp80) cc_final: 0.6025 (ttm-80) REVERT: B 249 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7759 (mm-30) REVERT: L 82 GLU cc_start: 0.8388 (pm20) cc_final: 0.8060 (pm20) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.0790 time to fit residues: 8.2048 Evaluate side-chains 85 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112369 restraints weight = 6238.216| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.72 r_work: 0.3185 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4891 Z= 0.108 Angle : 0.523 7.392 6656 Z= 0.269 Chirality : 0.041 0.160 763 Planarity : 0.004 0.036 826 Dihedral : 4.591 25.610 697 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.40 % Allowed : 18.04 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.04 (0.35), residues: 620 helix: 2.04 (0.30), residues: 311 sheet: 0.74 (0.59), residues: 83 loop : -1.32 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 208 TYR 0.011 0.001 TYR H 33 PHE 0.008 0.001 PHE L 72 TRP 0.021 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 4888) covalent geometry : angle 0.52169 / 0.27 ( 6650) SS BOND : bond 0.00394 / 0.20 ( 3) SS BOND : angle 1.11959 / 0.70 ( 6) hydrogen bonds : bond 0.02934 / 1.96 ( 279) hydrogen bonds : angle 3.72433 / 2.64 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.157 Fit side-chains REVERT: B 168 ARG cc_start: 0.6545 (ttp80) cc_final: 0.6141 (ttm-80) REVERT: B 183 MET cc_start: 0.7800 (mtt) cc_final: 0.7472 (mtp) REVERT: B 232 TYR cc_start: 0.6746 (t80) cc_final: 0.6493 (t80) REVERT: B 249 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7778 (mm-30) REVERT: H 6 GLN cc_start: 0.7198 (pp30) cc_final: 0.6992 (pp30) REVERT: L 82 GLU cc_start: 0.8349 (pm20) cc_final: 0.8065 (pm20) outliers start: 7 outliers final: 7 residues processed: 85 average time/residue: 0.0750 time to fit residues: 8.0734 Evaluate side-chains 85 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113857 restraints weight = 6152.687| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.70 r_work: 0.3197 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4891 Z= 0.107 Angle : 0.514 7.401 6656 Z= 0.264 Chirality : 0.041 0.158 763 Planarity : 0.004 0.038 826 Dihedral : 4.425 19.819 697 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.80 % Allowed : 17.84 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.35), residues: 620 helix: 2.07 (0.30), residues: 311 sheet: 0.75 (0.59), residues: 83 loop : -1.31 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.011 0.001 TYR H 33 PHE 0.014 0.001 PHE B 212 TRP 0.021 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 4888) covalent geometry : angle 0.51274 / 0.26 ( 6650) SS BOND : bond 0.00395 / 0.20 ( 3) SS BOND : angle 1.10761 / 0.70 ( 6) hydrogen bonds : bond 0.02911 / 1.95 ( 279) hydrogen bonds : angle 3.69655 / 2.62 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1158.93 seconds wall clock time: 20 minutes 31.24 seconds (1231.24 seconds total)