Starting phenix.real_space_refine on Tue Aug 4 16:07:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rh3_53956/08_2026/9rh3_53956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rh3_53956/08_2026/9rh3_53956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rh3_53956/08_2026/9rh3_53956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rh3_53956/08_2026/9rh3_53956.map" model { file = "/net/cci-nas-00/data/ceres_data/9rh3_53956/08_2026/9rh3_53956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rh3_53956/08_2026/9rh3_53956.cif" } resolution = 2.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3024 2.51 5 N 758 2.21 5 O 838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 4640 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2917 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Time building chain proxies: 1.26, per 1000 atoms: 0.27 Number of scatterers: 4640 At special positions: 0 Unit cell: (67.797, 77.004, 101.277, 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 20 16.00 O 838 8.00 N 758 7.00 C 3024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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: 0.38 Conformation dependent library (CDL) restraints added in 180.4 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 53.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 removed outlier: 4.234A pdb=" N GLY A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.633A pdb=" N GLY A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TRP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 Processing helix chain 'A' and resid 90 through 117 removed outlier: 4.809A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.552A pdb=" N VAL A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 4.016A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.524A pdb=" N GLU A 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 126 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.007A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.580A pdb=" N LYS A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.669A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.774A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.759A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.952A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6 removed outlier: 5.933A pdb=" N ALA B 16 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.487A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.657A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS B 98 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.572A pdb=" N GLN C 37 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 822 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: 0.80 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1347 1.33 - 1.45: 737 1.45 - 1.57: 2627 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 4744 Sorted by residual: bond pdb=" C ALA A 248 " pdb=" N LYS A 249 " ideal model delta sigma weight residual 1.334 1.299 0.035 1.46e-02 4.69e+03 5.88e+00 bond pdb=" CA LYS C 60 " pdb=" C LYS C 60 " ideal model delta sigma weight residual 1.522 1.550 -0.028 1.43e-02 4.89e+03 3.75e+00 bond pdb=" C LYS A 249 " pdb=" O LYS A 249 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.69e+00 bond pdb=" N LYS A 249 " pdb=" CA LYS A 249 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.30e-02 5.92e+03 1.81e+00 bond pdb=" C LYS C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.332 1.346 -0.014 1.12e-02 7.97e+03 1.63e+00 ... (remaining 4739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 6198 1.19 - 2.38: 185 2.38 - 3.57: 46 3.57 - 4.76: 11 4.76 - 5.96: 11 Bond angle restraints: 6451 Sorted by residual: angle pdb=" C ILE A 106 " pdb=" N VAL A 107 " pdb=" CA VAL A 107 " ideal model delta sigma weight residual 120.24 122.20 -1.96 6.30e-01 2.52e+00 9.64e+00 angle pdb=" C GLU B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 123.15 119.48 3.67 1.21e+00 6.83e-01 9.20e+00 angle pdb=" C PRO C 59 " pdb=" N LYS C 60 " pdb=" CA LYS C 60 " ideal model delta sigma weight residual 120.99 126.44 -5.45 1.86e+00 2.89e-01 8.59e+00 angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 112.13 115.84 -3.71 1.34e+00 5.57e-01 7.68e+00 angle pdb=" N ASP B 104 " pdb=" CA ASP B 104 " pdb=" C ASP B 104 " ideal model delta sigma weight residual 110.80 116.46 -5.66 2.13e+00 2.20e-01 7.06e+00 ... (remaining 6446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 2552 17.60 - 35.20: 159 35.20 - 52.79: 58 52.79 - 70.39: 5 70.39 - 87.99: 4 Dihedral angle restraints: 2778 sinusoidal: 1034 harmonic: 1744 Sorted by residual: dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 54.31 38.69 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CA ASN B 103 " pdb=" C ASN B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 2775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 535 0.037 - 0.074: 174 0.074 - 0.111: 45 0.111 - 0.148: 7 0.148 - 0.185: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA THR C 7 " pdb=" N THR C 7 " pdb=" C THR C 7 " pdb=" CB THR C 7 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL A 148 " pdb=" N VAL A 148 " pdb=" C VAL A 148 " pdb=" CB VAL A 148 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 759 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 35 " 0.008 2.00e-02 2.50e+03 8.49e-03 1.80e+00 pdb=" CG TRP C 35 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 35 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 35 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 35 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 35 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 35 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 35 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 107 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 108 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 136 " -0.001 2.00e-02 2.50e+03 7.43e-03 9.67e-01 pdb=" CG PHE A 136 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 136 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 136 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 136 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 136 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 136 " 0.001 2.00e-02 2.50e+03 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1263 2.81 - 3.33: 4347 3.33 - 3.85: 7792 3.85 - 4.38: 9133 4.38 - 4.90: 15846 Nonbonded interactions: 38381 Sorted by model distance: nonbonded pdb=" NZ LYS B 23 " pdb=" O SER B 76 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR A 38 " pdb=" O PHE A 269 " model vdw 2.310 3.040 nonbonded pdb=" NH2 ARG A 203 " pdb=" O LYS A 240 " model vdw 2.330 3.120 nonbonded pdb=" OD2 ASP B 73 " pdb=" OG SER B 76 " model vdw 2.337 3.040 nonbonded pdb=" NZ LYS A 57 " pdb=" OD2 ASP A 65 " model vdw 2.375 3.120 ... (remaining 38376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 0.037 4746 Z= 0.172 Angle : 0.582 5.955 6455 Z= 0.320 Chirality : 0.039 0.185 762 Planarity : 0.003 0.027 794 Dihedral : 13.642 87.987 1660 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.20 % Allowed : 9.35 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.92 (0.34), residues: 606 helix: 0.86 (0.29), residues: 279 sheet: 1.16 (0.44), residues: 132 loop : 0.04 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.012 0.001 TYR C 49 PHE 0.014 0.002 PHE A 136 TRP 0.021 0.002 TRP C 35 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 4744) covalent geometry : angle 0.58231 / 0.32 ( 6451) SS BOND : bond 0.00152 / 0.07 ( 2) SS BOND : angle 0.59041 / 0.30 ( 4) hydrogen bonds : bond 0.21294 / 14.45 ( 286) hydrogen bonds : angle 8.04431 / 5.88 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.176 Fit side-chains REVERT: A 28 MET cc_start: 0.8710 (mmm) cc_final: 0.7793 (mmp) REVERT: A 181 MET cc_start: 0.8172 (mmm) cc_final: 0.7935 (mmp) REVERT: A 240 LYS cc_start: 0.5165 (mppt) cc_final: 0.3123 (mptt) REVERT: A 241 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 250 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7307 (tmm160) REVERT: A 321 GLU cc_start: 0.7925 (tt0) cc_final: 0.7516 (pp20) REVERT: A 339 PHE cc_start: 0.8750 (t80) cc_final: 0.8406 (t80) REVERT: A 341 MET cc_start: 0.8844 (mmm) cc_final: 0.8644 (tpp) REVERT: A 356 GLU cc_start: 0.7963 (tt0) cc_final: 0.7711 (tt0) REVERT: A 359 ASN cc_start: 0.8389 (t0) cc_final: 0.7567 (m-40) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.5916 time to fit residues: 51.0282 Evaluate side-chains 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 58 ASN A 177 ASN A 359 ASN B 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102363 restraints weight = 5213.166| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.25 r_work: 0.2960 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4746 Z= 0.117 Angle : 0.533 6.928 6455 Z= 0.278 Chirality : 0.039 0.190 762 Planarity : 0.003 0.023 794 Dihedral : 4.400 21.610 652 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.83 % Allowed : 9.76 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.78 (0.34), residues: 606 helix: 1.97 (0.30), residues: 282 sheet: 1.34 (0.46), residues: 128 loop : -0.04 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.013 0.001 TYR C 49 PHE 0.013 0.001 PHE A 136 TRP 0.015 0.001 TRP C 35 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 4744) covalent geometry : angle 0.53328 / 0.28 ( 6451) SS BOND : bond 0.00385 / 0.18 ( 2) SS BOND : angle 0.52995 / 0.25 ( 4) hydrogen bonds : bond 0.04543 / 3.24 ( 286) hydrogen bonds : angle 5.32835 / 3.92 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.172 Fit side-chains REVERT: A 28 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7939 (mmp) REVERT: A 55 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8584 (tp) REVERT: A 240 LYS cc_start: 0.5731 (mppt) cc_final: 0.3294 (mptt) REVERT: A 241 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8174 (mt-10) REVERT: A 250 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7504 (ttt-90) REVERT: A 321 GLU cc_start: 0.8267 (tt0) cc_final: 0.7721 (pp20) REVERT: A 359 ASN cc_start: 0.8348 (t0) cc_final: 0.7663 (m-40) outliers start: 9 outliers final: 3 residues processed: 75 average time/residue: 0.6056 time to fit residues: 47.0888 Evaluate side-chains 70 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain C residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.167113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.094878 restraints weight = 5123.161| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.29 r_work: 0.2771 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4746 Z= 0.145 Angle : 0.542 7.363 6455 Z= 0.276 Chirality : 0.040 0.183 762 Planarity : 0.003 0.023 794 Dihedral : 4.471 21.854 652 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.24 % Allowed : 11.59 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.70 (0.34), residues: 606 helix: 1.93 (0.30), residues: 292 sheet: 1.27 (0.47), residues: 118 loop : -0.15 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.012 0.001 TYR C 49 PHE 0.014 0.001 PHE A 136 TRP 0.018 0.002 TRP C 35 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 4744) covalent geometry : angle 0.54250 / 0.28 ( 6451) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 0.14699 / 0.08 ( 4) hydrogen bonds : bond 0.04220 / 3.01 ( 286) hydrogen bonds : angle 4.95563 / 3.68 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.179 Fit side-chains REVERT: A 28 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7945 (mmp) REVERT: A 55 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 78 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8265 (tp30) REVERT: A 240 LYS cc_start: 0.6345 (mppt) cc_final: 0.3594 (ttmm) REVERT: A 250 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.7514 (ttt-90) REVERT: A 321 GLU cc_start: 0.8320 (tt0) cc_final: 0.7978 (pt0) REVERT: A 359 ASN cc_start: 0.8312 (t0) cc_final: 0.7526 (m-40) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.6109 time to fit residues: 41.8552 Evaluate side-chains 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain C residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096218 restraints weight = 5090.249| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.28 r_work: 0.2772 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4746 Z= 0.121 Angle : 0.505 6.791 6455 Z= 0.258 Chirality : 0.039 0.176 762 Planarity : 0.003 0.023 794 Dihedral : 4.314 20.926 652 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.64 % Allowed : 12.40 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.76 (0.34), residues: 606 helix: 2.00 (0.30), residues: 293 sheet: 1.32 (0.46), residues: 118 loop : -0.16 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.012 0.001 TYR C 49 PHE 0.012 0.001 PHE A 136 TRP 0.016 0.001 TRP C 35 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 4744) covalent geometry : angle 0.50545 / 0.26 ( 6451) SS BOND : bond 0.00149 / 0.07 ( 2) SS BOND : angle 0.26506 / 0.11 ( 4) hydrogen bonds : bond 0.03769 / 2.72 ( 286) hydrogen bonds : angle 4.78749 / 3.56 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.177 Fit side-chains REVERT: A 28 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7900 (mmp) REVERT: A 55 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 240 LYS cc_start: 0.6293 (mppt) cc_final: 0.3254 (mppt) REVERT: A 250 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7432 (ttt-90) REVERT: A 321 GLU cc_start: 0.8297 (tt0) cc_final: 0.7953 (pt0) REVERT: A 359 ASN cc_start: 0.8312 (t0) cc_final: 0.7472 (m-40) outliers start: 13 outliers final: 6 residues processed: 67 average time/residue: 0.5771 time to fit residues: 40.2020 Evaluate side-chains 69 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.168360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096534 restraints weight = 5146.537| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.27 r_work: 0.2769 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4746 Z= 0.112 Angle : 0.493 6.509 6455 Z= 0.252 Chirality : 0.039 0.174 762 Planarity : 0.003 0.023 794 Dihedral : 4.249 20.277 652 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.24 % Allowed : 12.80 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.87 (0.34), residues: 606 helix: 2.08 (0.30), residues: 293 sheet: 1.32 (0.46), residues: 118 loop : -0.07 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.011 0.001 TYR C 49 PHE 0.009 0.001 PHE A 72 TRP 0.016 0.001 TRP C 35 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 4744) covalent geometry : angle 0.49343 / 0.25 ( 6451) SS BOND : bond 0.00149 / 0.07 ( 2) SS BOND : angle 0.19178 / 0.10 ( 4) hydrogen bonds : bond 0.03632 / 2.63 ( 286) hydrogen bonds : angle 4.72170 / 3.53 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.194 Fit side-chains REVERT: A 28 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7912 (mmp) REVERT: A 55 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 240 LYS cc_start: 0.6301 (mppt) cc_final: 0.3254 (mppt) REVERT: A 250 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.7430 (ttt-90) REVERT: A 321 GLU cc_start: 0.8293 (tt0) cc_final: 0.7952 (pt0) REVERT: A 359 ASN cc_start: 0.8302 (t0) cc_final: 0.7454 (m-40) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.6062 time to fit residues: 41.5044 Evaluate side-chains 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.094385 restraints weight = 5152.010| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.30 r_work: 0.2726 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4746 Z= 0.150 Angle : 0.532 8.683 6455 Z= 0.268 Chirality : 0.040 0.176 762 Planarity : 0.003 0.022 794 Dihedral : 4.393 22.210 652 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.25 % Allowed : 12.40 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.79 (0.34), residues: 606 helix: 1.98 (0.30), residues: 292 sheet: 1.31 (0.47), residues: 118 loop : -0.06 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 13 TYR 0.013 0.001 TYR C 49 PHE 0.013 0.001 PHE A 72 TRP 0.025 0.002 TRP C 35 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 4744) covalent geometry : angle 0.53218 / 0.27 ( 6451) SS BOND : bond 0.00172 / 0.08 ( 2) SS BOND : angle 0.33551 / 0.17 ( 4) hydrogen bonds : bond 0.04014 / 2.87 ( 286) hydrogen bonds : angle 4.74728 / 3.53 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.172 Fit side-chains REVERT: A 28 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7861 (mmp) REVERT: A 55 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 240 LYS cc_start: 0.6378 (mppt) cc_final: 0.3497 (ttmm) REVERT: A 250 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.7350 (ttt-90) REVERT: A 321 GLU cc_start: 0.8303 (tt0) cc_final: 0.7922 (pt0) REVERT: A 359 ASN cc_start: 0.8275 (t0) cc_final: 0.7421 (m-40) outliers start: 16 outliers final: 9 residues processed: 68 average time/residue: 0.6081 time to fit residues: 42.9891 Evaluate side-chains 70 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 29 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 61 ASN C 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.096238 restraints weight = 5130.544| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.27 r_work: 0.2765 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4746 Z= 0.114 Angle : 0.497 8.171 6455 Z= 0.252 Chirality : 0.039 0.174 762 Planarity : 0.003 0.023 794 Dihedral : 4.274 20.667 652 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.05 % Allowed : 13.41 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.82 (0.34), residues: 606 helix: 1.98 (0.30), residues: 295 sheet: 1.32 (0.47), residues: 118 loop : -0.02 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 381 TYR 0.011 0.001 TYR C 49 PHE 0.009 0.001 PHE A 72 TRP 0.023 0.001 TRP C 35 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 4744) covalent geometry : angle 0.49707 / 0.25 ( 6451) SS BOND : bond 0.00210 / 0.10 ( 2) SS BOND : angle 0.20253 / 0.09 ( 4) hydrogen bonds : bond 0.03592 / 2.60 ( 286) hydrogen bonds : angle 4.66166 / 3.47 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.171 Fit side-chains REVERT: A 28 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7914 (mmp) REVERT: A 54 GLU cc_start: 0.8382 (tt0) cc_final: 0.8158 (tt0) REVERT: A 55 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8489 (tp) REVERT: A 240 LYS cc_start: 0.6311 (mppt) cc_final: 0.3509 (ttmm) REVERT: A 245 ARG cc_start: 0.7374 (tmt170) cc_final: 0.7150 (tmt170) REVERT: A 250 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.7475 (tmm160) REVERT: A 321 GLU cc_start: 0.8326 (tt0) cc_final: 0.7933 (pt0) REVERT: A 359 ASN cc_start: 0.8312 (t0) cc_final: 0.7499 (m-40) outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 0.5940 time to fit residues: 43.1398 Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 29 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.166421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.093850 restraints weight = 5215.288| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.31 r_work: 0.2730 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4746 Z= 0.166 Angle : 0.543 7.886 6455 Z= 0.274 Chirality : 0.040 0.175 762 Planarity : 0.003 0.022 794 Dihedral : 4.446 22.873 652 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.44 % Allowed : 14.63 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.75 (0.33), residues: 606 helix: 2.01 (0.30), residues: 286 sheet: 1.25 (0.47), residues: 118 loop : -0.08 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.014 0.001 TYR C 49 PHE 0.015 0.002 PHE A 72 TRP 0.032 0.002 TRP C 35 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 4744) covalent geometry : angle 0.54326 / 0.27 ( 6451) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 0.18821 / 0.08 ( 4) hydrogen bonds : bond 0.04087 / 2.92 ( 286) hydrogen bonds : angle 4.76080 / 3.53 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.106 Fit side-chains REVERT: A 28 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7931 (mmp) REVERT: A 55 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 240 LYS cc_start: 0.6590 (mppt) cc_final: 0.3249 (ptpp) REVERT: A 245 ARG cc_start: 0.7387 (tmt170) cc_final: 0.7175 (tmt170) REVERT: A 250 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.7530 (tmm160) REVERT: A 321 GLU cc_start: 0.8352 (tt0) cc_final: 0.7942 (pt0) REVERT: A 359 ASN cc_start: 0.8344 (t0) cc_final: 0.7503 (m110) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.5941 time to fit residues: 41.2440 Evaluate side-chains 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.167576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096083 restraints weight = 5074.911| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.24 r_work: 0.2746 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4746 Z= 0.131 Angle : 0.521 7.840 6455 Z= 0.262 Chirality : 0.039 0.175 762 Planarity : 0.003 0.022 794 Dihedral : 4.374 21.670 652 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 14.84 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.72 (0.33), residues: 606 helix: 1.98 (0.30), residues: 289 sheet: 1.31 (0.48), residues: 112 loop : -0.13 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 46 TYR 0.012 0.001 TYR C 49 PHE 0.012 0.001 PHE A 72 TRP 0.034 0.002 TRP C 35 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 4744) covalent geometry : angle 0.52074 / 0.26 ( 6451) SS BOND : bond 0.00299 / 0.14 ( 2) SS BOND : angle 0.38760 / 0.19 ( 4) hydrogen bonds : bond 0.03762 / 2.71 ( 286) hydrogen bonds : angle 4.69561 / 3.49 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.188 Fit side-chains REVERT: A 28 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7889 (mmp) REVERT: A 54 GLU cc_start: 0.8391 (tt0) cc_final: 0.8186 (tt0) REVERT: A 55 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8488 (tp) REVERT: A 240 LYS cc_start: 0.6492 (mppt) cc_final: 0.3542 (ttmm) REVERT: A 245 ARG cc_start: 0.7327 (tmt170) cc_final: 0.7113 (tmt170) REVERT: A 250 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7414 (tmm160) REVERT: A 321 GLU cc_start: 0.8312 (tt0) cc_final: 0.7898 (pt0) REVERT: A 359 ASN cc_start: 0.8311 (t0) cc_final: 0.7454 (m-40) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.6127 time to fit residues: 42.6388 Evaluate side-chains 70 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098098 restraints weight = 5119.789| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.29 r_work: 0.2830 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4746 Z= 0.098 Angle : 0.489 7.625 6455 Z= 0.246 Chirality : 0.038 0.171 762 Planarity : 0.003 0.023 794 Dihedral : 4.152 20.988 652 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.83 % Allowed : 15.45 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.81 (0.34), residues: 606 helix: 2.03 (0.30), residues: 295 sheet: 1.37 (0.48), residues: 112 loop : -0.13 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.011 0.001 TYR C 49 PHE 0.008 0.001 PHE B 64 TRP 0.039 0.002 TRP C 35 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 4744) covalent geometry : angle 0.48875 / 0.25 ( 6451) SS BOND : bond 0.00283 / 0.13 ( 2) SS BOND : angle 0.35908 / 0.17 ( 4) hydrogen bonds : bond 0.03345 / 2.43 ( 286) hydrogen bonds : angle 4.59259 / 3.43 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.169 Fit side-chains REVERT: A 28 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.7901 (mmp) REVERT: A 55 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8480 (tp) REVERT: A 240 LYS cc_start: 0.6300 (mppt) cc_final: 0.3231 (ptpp) REVERT: A 245 ARG cc_start: 0.7372 (tmt170) cc_final: 0.7148 (tmt170) REVERT: A 250 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.7498 (tmm160) REVERT: A 321 GLU cc_start: 0.8341 (tt0) cc_final: 0.7959 (pt0) REVERT: A 359 ASN cc_start: 0.8368 (t0) cc_final: 0.7555 (m-40) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.5669 time to fit residues: 41.8828 Evaluate side-chains 73 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 8.9990 chunk 12 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102698 restraints weight = 5173.114| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.25 r_work: 0.2964 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4746 Z= 0.097 Angle : 0.490 7.605 6455 Z= 0.247 Chirality : 0.038 0.171 762 Planarity : 0.003 0.023 794 Dihedral : 4.105 20.044 652 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.63 % Allowed : 15.85 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.81 (0.34), residues: 606 helix: 2.07 (0.30), residues: 295 sheet: 1.22 (0.49), residues: 106 loop : -0.05 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.010 0.001 TYR C 49 PHE 0.008 0.001 PHE B 64 TRP 0.034 0.001 TRP C 35 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 4744) covalent geometry : angle 0.49024 / 0.25 ( 6451) SS BOND : bond 0.00634 / 0.30 ( 2) SS BOND : angle 0.21819 / 0.11 ( 4) hydrogen bonds : bond 0.03341 / 2.43 ( 286) hydrogen bonds : angle 4.55939 / 3.40 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.34 seconds wall clock time: 39 minutes 44.91 seconds (2384.91 seconds total)