Starting phenix.real_space_refine on Thu Oct 22 17:55:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26qj_80827/10_2026/26qj_80827.cif Found real_map, /net/cci-nas-00/data/ceres_data/26qj_80827/10_2026/26qj_80827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/26qj_80827/10_2026/26qj_80827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26qj_80827/10_2026/26qj_80827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/26qj_80827/10_2026/26qj_80827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26qj_80827/10_2026/26qj_80827.map" } resolution = 3.34 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= 0.002 sd= 0.096 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 27 5.16 5 C 2016 2.51 5 N 489 2.21 5 O 523 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3055 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3012 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'CLR': 1, 'NBV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.00, per 1000 atoms: 0.33 Number of scatterers: 3055 At special positions: 0 Unit cell: (63.448, 59.328, 84.872, 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 27 16.00 O 523 8.00 N 489 7.00 C 2016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.31 Conformation dependent library (CDL) restraints added in 125.5 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 706 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 61.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 3 through 37 Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.820A pdb=" N PHE A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 105 Processing helix chain 'A' and resid 122 through 135 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.500A pdb=" N THR A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.552A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.543A pdb=" N PHE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 314 through 339 removed outlier: 3.508A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 370 removed outlier: 4.083A pdb=" N ILE A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 8.290A pdb=" N ARG A 111 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 83 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 113 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 85 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 53 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 55 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS A 86 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 57 " --> pdb=" O CYS A 86 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER A 54 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N CYS A 143 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU A 56 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.252A pdb=" N MET A 258 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR A 173 " --> pdb=" O GLN A 259 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 483 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: 0.44 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 516 1.32 - 1.44: 833 1.44 - 1.57: 1746 1.57 - 1.69: 1 1.69 - 1.81: 44 Bond restraints: 3140 Sorted by residual: bond pdb=" C13 NBV A 402 " pdb=" N1 NBV A 402 " ideal model delta sigma weight residual 1.456 1.217 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C9 NBV A 402 " pdb=" O8 NBV A 402 " ideal model delta sigma weight residual 1.410 1.491 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" CZ ARG A 249 " pdb=" NH2 ARG A 249 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" CZ ARG A 177 " pdb=" NH2 ARG A 177 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.12e+01 bond pdb=" C10 NBV A 402 " pdb=" O1 NBV A 402 " ideal model delta sigma weight residual 1.409 1.475 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 3135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 3060 1.74 - 3.49: 979 3.49 - 5.23: 202 5.23 - 6.97: 20 6.97 - 8.72: 6 Bond angle restraints: 4267 Sorted by residual: angle pdb=" N ARG A 376 " pdb=" CA ARG A 376 " pdb=" C ARG A 376 " ideal model delta sigma weight residual 112.54 103.83 8.71 1.22e+00 6.72e-01 5.09e+01 angle pdb=" N LEU A 24 " pdb=" CA LEU A 24 " pdb=" C LEU A 24 " ideal model delta sigma weight residual 112.89 104.17 8.72 1.24e+00 6.50e-01 4.94e+01 angle pdb=" CA PHE A 250 " pdb=" CB PHE A 250 " pdb=" CG PHE A 250 " ideal model delta sigma weight residual 113.80 120.53 -6.73 1.00e+00 1.00e+00 4.52e+01 angle pdb=" N LEU A 4 " pdb=" CA LEU A 4 " pdb=" C LEU A 4 " ideal model delta sigma weight residual 111.28 104.53 6.75 1.09e+00 8.42e-01 3.84e+01 angle pdb=" N ARG A 249 " pdb=" CA ARG A 249 " pdb=" C ARG A 249 " ideal model delta sigma weight residual 110.24 118.65 -8.41 1.41e+00 5.03e-01 3.56e+01 ... (remaining 4262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 1817 24.82 - 49.64: 62 49.64 - 74.46: 8 74.46 - 99.28: 2 99.28 - 124.10: 3 Dihedral angle restraints: 1892 sinusoidal: 792 harmonic: 1100 Sorted by residual: dihedral pdb=" CA TRP A 248 " pdb=" C TRP A 248 " pdb=" N ARG A 249 " pdb=" CA ARG A 249 " ideal model delta harmonic sigma weight residual -180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 116 " pdb=" C GLY A 116 " pdb=" N LYS A 117 " pdb=" CA LYS A 117 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA VAL A 219 " pdb=" C VAL A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 1889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 303 0.071 - 0.142: 126 0.142 - 0.213: 29 0.213 - 0.284: 15 0.284 - 0.355: 5 Chirality restraints: 478 Sorted by residual: chirality pdb=" CA LEU A 128 " pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CB LEU A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB THR A 72 " pdb=" CA THR A 72 " pdb=" OG1 THR A 72 " pdb=" CG2 THR A 72 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA PRO A 151 " pdb=" N PRO A 151 " pdb=" C PRO A 151 " pdb=" CB PRO A 151 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 475 not shown) Planarity restraints: 519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 305 " 0.202 2.00e-02 2.50e+03 9.99e-02 2.49e+02 pdb=" CG TRP A 305 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A 305 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 305 " -0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP A 305 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A 305 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 305 " -0.132 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 305 " 0.105 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 305 " -0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP A 305 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 248 " 0.177 2.00e-02 2.50e+03 9.16e-02 2.10e+02 pdb=" CG TRP A 248 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 248 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 248 " -0.122 2.00e-02 2.50e+03 pdb=" NE1 TRP A 248 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 248 " -0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP A 248 " -0.120 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 248 " 0.083 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 248 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 248 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 326 " -0.165 2.00e-02 2.50e+03 8.78e-02 1.93e+02 pdb=" CG TRP A 326 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 326 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 326 " 0.094 2.00e-02 2.50e+03 pdb=" NE1 TRP A 326 " 0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP A 326 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP A 326 " 0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 326 " -0.101 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 326 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP A 326 " -0.106 2.00e-02 2.50e+03 ... (remaining 516 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1228 2.92 - 3.41: 3144 3.41 - 3.91: 5183 3.91 - 4.40: 5652 4.40 - 4.90: 9618 Nonbonded interactions: 24825 Sorted by model distance: nonbonded pdb=" O ARG A 383 " pdb=" C CYS A 384 " model vdw 2.425 3.270 nonbonded pdb=" OD2 ASP A 236 " pdb=" C14 NBV A 402 " model vdw 2.428 3.440 nonbonded pdb=" O PRO A 51 " pdb=" OH TYR A 78 " model vdw 2.467 3.040 nonbonded pdb=" N LEU A 24 " pdb=" N MET A 25 " model vdw 2.495 2.560 nonbonded pdb=" N ARG A 376 " pdb=" N THR A 377 " model vdw 2.516 2.560 ... (remaining 24820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.910 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.012 0.239 3140 Z= 0.750 Angle : 1.743 8.718 4267 Z= 1.184 Chirality : 0.093 0.355 478 Planarity : 0.014 0.110 519 Dihedral : 14.027 124.103 1186 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.12 % Allowed : 5.00 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.38), residues: 374 helix: -1.24 (0.30), residues: 212 sheet: -1.90 (0.70), residues: 47 loop : -1.83 (0.53), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 312 TYR 0.104 0.018 TYR A 349 PHE 0.060 0.010 PHE A 238 TRP 0.202 0.036 TRP A 305 HIS 0.015 0.004 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.01237 / 0.75 ( 3140) covalent geometry : angle 1.74327 / 1.18 ( 4267) hydrogen bonds : bond 0.19922 / 13.17 ( 164) hydrogen bonds : angle 8.19144 / 6.10 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.112 Fit side-chains REVERT: A 89 ASP cc_start: 0.7687 (t0) cc_final: 0.7226 (m-30) REVERT: A 160 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7452 (mp10) REVERT: A 191 THR cc_start: 0.7506 (m) cc_final: 0.7110 (p) REVERT: A 192 SER cc_start: 0.7467 (t) cc_final: 0.7170 (p) REVERT: A 211 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7528 (mtp) REVERT: A 249 ARG cc_start: 0.6827 (ptm160) cc_final: 0.6151 (ttt90) REVERT: A 316 MET cc_start: 0.6563 (tpt) cc_final: 0.6085 (ttp) outliers start: 10 outliers final: 3 residues processed: 113 average time/residue: 0.0643 time to fit residues: 8.6427 Evaluate side-chains 75 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 382 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 13] chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN A 231 GLN A 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.164013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125375 restraints weight = 3614.697| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.28 r_work: 0.3239 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3140 Z= 0.142 Angle : 0.660 10.683 4267 Z= 0.336 Chirality : 0.043 0.130 478 Planarity : 0.005 0.036 519 Dihedral : 9.979 81.916 507 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.12 % Allowed : 13.44 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.43), residues: 374 helix: 1.50 (0.36), residues: 209 sheet: -0.77 (0.83), residues: 37 loop : -1.40 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.019 0.002 TYR A 188 PHE 0.020 0.002 PHE A 327 TRP 0.037 0.002 TRP A 248 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 3140) covalent geometry : angle 0.65989 / 0.34 ( 4267) hydrogen bonds : bond 0.04283 / 2.88 ( 164) hydrogen bonds : angle 5.02050 / 3.55 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.073 Fit side-chains REVERT: A 111 ARG cc_start: 0.6785 (ttt180) cc_final: 0.6491 (ttt180) REVERT: A 211 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: A 237 TYR cc_start: 0.8803 (t80) cc_final: 0.8514 (t80) REVERT: A 249 ARG cc_start: 0.7073 (ptm160) cc_final: 0.5591 (tpt-90) REVERT: A 320 MET cc_start: 0.7571 (mtt) cc_final: 0.7312 (mtm) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 0.0666 time to fit residues: 5.8422 Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [27, 16, 17, 7, 22, 32, 34, 4, 0, 2, 8] chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN ** A 282 ASN ** 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 = 0.3756 r_free = 0.3756 target = 0.161840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122309 restraints weight = 3679.130| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.34 r_work: 0.3190 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3140 Z= 0.143 Angle : 0.619 10.696 4267 Z= 0.307 Chirality : 0.041 0.123 478 Planarity : 0.004 0.035 519 Dihedral : 7.211 45.015 504 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.44 % Allowed : 13.12 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.43), residues: 374 helix: 1.78 (0.35), residues: 210 sheet: -0.65 (0.83), residues: 37 loop : -1.24 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 335 TYR 0.017 0.002 TYR A 188 PHE 0.014 0.002 PHE A 327 TRP 0.030 0.002 TRP A 248 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3140) covalent geometry : angle 0.61906 / 0.31 ( 4267) hydrogen bonds : bond 0.04124 / 2.78 ( 164) hydrogen bonds : angle 4.59284 / 3.24 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.106 Fit side-chains REVERT: A 1 MET cc_start: 0.5580 (mmt) cc_final: 0.5069 (mmt) REVERT: A 100 LYS cc_start: 0.7388 (mmtm) cc_final: 0.6957 (mmtt) REVERT: A 101 LEU cc_start: 0.8280 (mm) cc_final: 0.7935 (mm) REVERT: A 111 ARG cc_start: 0.6845 (ttt180) cc_final: 0.6557 (ttt180) REVERT: A 118 LYS cc_start: 0.8512 (tptp) cc_final: 0.8265 (tptp) REVERT: A 215 MET cc_start: 0.8227 (mtm) cc_final: 0.7943 (mtt) REVERT: A 237 TYR cc_start: 0.8857 (t80) cc_final: 0.8400 (t80) REVERT: A 249 ARG cc_start: 0.7074 (ptm160) cc_final: 0.5473 (tpt-90) REVERT: A 320 MET cc_start: 0.7616 (mtt) cc_final: 0.6752 (ttt) REVERT: A 356 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7346 (ttp80) outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 0.0606 time to fit residues: 5.3133 Evaluate side-chains 67 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [5, 2, 22, 13, 26, 36, 7, 21, 6, 8, 17] chunk 5 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 21 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** 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 = 0.3776 r_free = 0.3776 target = 0.163090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123931 restraints weight = 3672.970| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.36 r_work: 0.3226 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3140 Z= 0.107 Angle : 0.528 6.344 4267 Z= 0.268 Chirality : 0.039 0.122 478 Planarity : 0.004 0.042 519 Dihedral : 5.472 34.658 499 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.75 % Allowed : 13.75 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.43), residues: 374 helix: 2.09 (0.35), residues: 207 sheet: -0.46 (0.83), residues: 37 loop : -0.92 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.018 0.002 TYR A 188 PHE 0.024 0.001 PHE A 311 TRP 0.023 0.002 TRP A 248 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 3140) covalent geometry : angle 0.52763 / 0.27 ( 4267) hydrogen bonds : bond 0.03608 / 2.45 ( 164) hydrogen bonds : angle 4.55184 / 3.18 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.067 Fit side-chains REVERT: A 1 MET cc_start: 0.5446 (mmt) cc_final: 0.4959 (mmt) REVERT: A 100 LYS cc_start: 0.7484 (mmtm) cc_final: 0.7045 (mmtt) REVERT: A 101 LEU cc_start: 0.8270 (mm) cc_final: 0.7949 (mm) REVERT: A 111 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6757 (ttt180) REVERT: A 118 LYS cc_start: 0.8442 (tptp) cc_final: 0.8200 (tptp) REVERT: A 144 ASP cc_start: 0.7971 (t0) cc_final: 0.7692 (m-30) REVERT: A 233 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7890 (mm) REVERT: A 237 TYR cc_start: 0.8778 (t80) cc_final: 0.8039 (t80) REVERT: A 249 ARG cc_start: 0.7058 (ptm160) cc_final: 0.5473 (tpt170) REVERT: A 258 MET cc_start: 0.8533 (tpp) cc_final: 0.8273 (tpp) REVERT: A 273 MET cc_start: 0.8427 (mmm) cc_final: 0.8226 (mmm) REVERT: A 320 MET cc_start: 0.7571 (mtt) cc_final: 0.6704 (ttt) REVERT: A 356 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7281 (ttp80) outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 0.0605 time to fit residues: 5.0826 Evaluate side-chains 69 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [26, 32, 4, 11, 36, 10, 20, 23, 27, 18, 13] chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123926 restraints weight = 3706.895| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.38 r_work: 0.3221 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3140 Z= 0.107 Angle : 0.517 7.776 4267 Z= 0.262 Chirality : 0.039 0.120 478 Planarity : 0.004 0.033 519 Dihedral : 5.366 39.316 499 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.12 % Allowed : 15.94 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.42), residues: 374 helix: 1.88 (0.35), residues: 214 sheet: -0.45 (0.83), residues: 37 loop : -1.00 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.015 0.001 TYR A 188 PHE 0.015 0.001 PHE A 327 TRP 0.021 0.002 TRP A 248 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 3140) covalent geometry : angle 0.51698 / 0.26 ( 4267) hydrogen bonds : bond 0.03489 / 2.35 ( 164) hydrogen bonds : angle 4.44740 / 3.09 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.113 Fit side-chains REVERT: A 1 MET cc_start: 0.5626 (mmt) cc_final: 0.5118 (mmt) REVERT: A 78 TYR cc_start: 0.7545 (t80) cc_final: 0.7328 (t80) REVERT: A 100 LYS cc_start: 0.7504 (mmtm) cc_final: 0.7070 (mmtt) REVERT: A 101 LEU cc_start: 0.8245 (mm) cc_final: 0.7893 (mm) REVERT: A 144 ASP cc_start: 0.7984 (t0) cc_final: 0.7640 (m-30) REVERT: A 233 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7912 (mm) REVERT: A 248 TRP cc_start: 0.3586 (OUTLIER) cc_final: 0.2385 (p-90) REVERT: A 249 ARG cc_start: 0.6982 (ptm160) cc_final: 0.5293 (tpt-90) REVERT: A 258 MET cc_start: 0.8490 (tpp) cc_final: 0.8239 (tpp) REVERT: A 273 MET cc_start: 0.8479 (mmm) cc_final: 0.8276 (mmm) REVERT: A 320 MET cc_start: 0.7613 (mtt) cc_final: 0.6736 (ttt) REVERT: A 356 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7278 (ttp80) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.0587 time to fit residues: 5.1584 Evaluate side-chains 73 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 248 TRP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [20, 30, 9, 32, 11, 31, 22, 8, 2, 10, 17] chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 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 = 0.3726 r_free = 0.3726 target = 0.158424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118911 restraints weight = 3644.094| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.31 r_work: 0.3162 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3140 Z= 0.154 Angle : 0.565 7.538 4267 Z= 0.286 Chirality : 0.041 0.125 478 Planarity : 0.004 0.032 519 Dihedral : 5.404 39.142 499 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.69 % Allowed : 16.56 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.43), residues: 374 helix: 1.94 (0.35), residues: 206 sheet: -0.45 (0.84), residues: 37 loop : -0.62 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.014 0.002 TYR A 188 PHE 0.031 0.002 PHE A 311 TRP 0.023 0.002 TRP A 248 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 3140) covalent geometry : angle 0.56540 / 0.29 ( 4267) hydrogen bonds : bond 0.03928 / 2.61 ( 164) hydrogen bonds : angle 4.52743 / 3.15 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5275 (mmt) cc_final: 0.4822 (mmt) REVERT: A 100 LYS cc_start: 0.7611 (mmtm) cc_final: 0.7207 (mmtt) REVERT: A 101 LEU cc_start: 0.8254 (mm) cc_final: 0.7872 (mm) REVERT: A 144 ASP cc_start: 0.8065 (t0) cc_final: 0.7709 (m-30) REVERT: A 215 MET cc_start: 0.8452 (mtm) cc_final: 0.8106 (mtt) REVERT: A 233 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7906 (mm) REVERT: A 237 TYR cc_start: 0.8559 (t80) cc_final: 0.7666 (t80) REVERT: A 249 ARG cc_start: 0.7146 (ptm160) cc_final: 0.5452 (tpt-90) REVERT: A 273 MET cc_start: 0.8485 (mmm) cc_final: 0.8258 (mmm) REVERT: A 320 MET cc_start: 0.7648 (mtt) cc_final: 0.6773 (ttt) REVERT: A 356 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7299 (ttp80) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.0570 time to fit residues: 5.0395 Evaluate side-chains 72 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 248 TRP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [35, 31, 1, 34, 14, 23, 28, 3, 0, 16, 24] chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN ** A 333 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 = 0.3745 r_free = 0.3745 target = 0.160613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121242 restraints weight = 3709.420| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.32 r_work: 0.3196 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3140 Z= 0.115 Angle : 0.534 6.888 4267 Z= 0.267 Chirality : 0.039 0.121 478 Planarity : 0.004 0.031 519 Dihedral : 5.174 39.031 499 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.06 % Allowed : 18.75 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.44), residues: 374 helix: 2.09 (0.35), residues: 207 sheet: -0.37 (0.87), residues: 37 loop : -0.47 (0.54), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.014 0.001 TYR A 188 PHE 0.030 0.002 PHE A 311 TRP 0.022 0.002 TRP A 248 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 3140) covalent geometry : angle 0.53361 / 0.27 ( 4267) hydrogen bonds : bond 0.03503 / 2.35 ( 164) hydrogen bonds : angle 4.51722 / 3.12 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.083 Fit side-chains REVERT: A 1 MET cc_start: 0.5393 (mmt) cc_final: 0.4900 (mmt) REVERT: A 100 LYS cc_start: 0.7657 (mmtm) cc_final: 0.7249 (mmtt) REVERT: A 101 LEU cc_start: 0.8246 (mm) cc_final: 0.7877 (mm) REVERT: A 144 ASP cc_start: 0.8040 (t0) cc_final: 0.7672 (m-30) REVERT: A 233 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 248 TRP cc_start: 0.3974 (OUTLIER) cc_final: 0.2410 (p-90) REVERT: A 320 MET cc_start: 0.7600 (mtt) cc_final: 0.6721 (ttt) REVERT: A 356 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7324 (ttp80) REVERT: A 359 MET cc_start: 0.7654 (ttt) cc_final: 0.7346 (ttt) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.0388 time to fit residues: 3.5865 Evaluate side-chains 75 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 248 TRP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 375 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [15, 7, 19, 4, 16, 17, 12, 29, 8, 0, 36] chunk 15 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 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 = 0.3734 r_free = 0.3734 target = 0.159474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120046 restraints weight = 3755.686| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.32 r_work: 0.3170 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3140 Z= 0.145 Angle : 0.552 6.720 4267 Z= 0.281 Chirality : 0.040 0.123 478 Planarity : 0.004 0.031 519 Dihedral : 5.244 40.411 499 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.06 % Allowed : 19.38 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.44), residues: 374 helix: 2.06 (0.35), residues: 206 sheet: -1.14 (0.78), residues: 47 loop : -0.44 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.020 0.002 TYR A 188 PHE 0.031 0.002 PHE A 311 TRP 0.022 0.002 TRP A 248 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3140) covalent geometry : angle 0.55153 / 0.28 ( 4267) hydrogen bonds : bond 0.03891 / 2.59 ( 164) hydrogen bonds : angle 4.54378 / 3.14 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5348 (mmt) cc_final: 0.4896 (mmt) REVERT: A 100 LYS cc_start: 0.7714 (mmtm) cc_final: 0.7303 (mmtt) REVERT: A 101 LEU cc_start: 0.8265 (mm) cc_final: 0.7854 (mm) REVERT: A 144 ASP cc_start: 0.8115 (t0) cc_final: 0.7734 (m-30) REVERT: A 233 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7588 (mm) REVERT: A 237 TYR cc_start: 0.8504 (t80) cc_final: 0.7493 (t80) REVERT: A 249 ARG cc_start: 0.7083 (ptm160) cc_final: 0.5433 (tpt-90) REVERT: A 320 MET cc_start: 0.7638 (mtt) cc_final: 0.6783 (ttt) REVERT: A 356 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7347 (ttp80) REVERT: A 359 MET cc_start: 0.7730 (ttt) cc_final: 0.7457 (ttt) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.0560 time to fit residues: 5.1034 Evaluate side-chains 74 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 248 TRP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 375 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [10, 8, 34, 30, 24, 9, 13, 19, 5, 32, 7] chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 30 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.162346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123471 restraints weight = 3747.478| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.26 r_work: 0.3219 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3140 Z= 0.108 Angle : 0.519 6.460 4267 Z= 0.264 Chirality : 0.039 0.123 478 Planarity : 0.004 0.033 519 Dihedral : 5.076 39.730 499 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.44 % Allowed : 20.62 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.44), residues: 374 helix: 2.22 (0.36), residues: 207 sheet: -1.10 (0.79), residues: 47 loop : -0.30 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 272 TYR 0.023 0.001 TYR A 188 PHE 0.033 0.002 PHE A 311 TRP 0.021 0.002 TRP A 248 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 3140) covalent geometry : angle 0.51863 / 0.26 ( 4267) hydrogen bonds : bond 0.03438 / 2.29 ( 164) hydrogen bonds : angle 4.52257 / 3.11 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.113 Fit side-chains REVERT: A 1 MET cc_start: 0.5388 (mmt) cc_final: 0.4881 (mmt) REVERT: A 100 LYS cc_start: 0.7688 (mmtm) cc_final: 0.7280 (mmtt) REVERT: A 101 LEU cc_start: 0.8284 (mm) cc_final: 0.7894 (mm) REVERT: A 144 ASP cc_start: 0.8014 (t0) cc_final: 0.7664 (m-30) REVERT: A 233 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7460 (mm) REVERT: A 237 TYR cc_start: 0.8516 (t80) cc_final: 0.7429 (t80) REVERT: A 248 TRP cc_start: 0.3876 (OUTLIER) cc_final: 0.2272 (p-90) REVERT: A 249 ARG cc_start: 0.6929 (ptm160) cc_final: 0.5316 (tpt-90) REVERT: A 316 MET cc_start: 0.6754 (mmp) cc_final: 0.6522 (mmp) REVERT: A 320 MET cc_start: 0.7587 (mtt) cc_final: 0.6731 (ttt) REVERT: A 356 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7296 (ttp80) REVERT: A 359 MET cc_start: 0.7606 (ttt) cc_final: 0.7392 (ttt) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.0577 time to fit residues: 5.2437 Evaluate side-chains 75 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 248 TRP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 375 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [5, 9, 31, 10, 25, 1, 14, 32, 36, 22, 8] chunk 5 optimal weight: 0.0040 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN ** A 333 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 = 0.3747 r_free = 0.3747 target = 0.160873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121113 restraints weight = 3689.145| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.36 r_work: 0.3189 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3140 Z= 0.125 Angle : 0.533 6.464 4267 Z= 0.274 Chirality : 0.039 0.121 478 Planarity : 0.004 0.036 519 Dihedral : 5.147 41.332 499 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.75 % Allowed : 20.31 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.44), residues: 374 helix: 2.20 (0.35), residues: 206 sheet: -1.00 (0.80), residues: 47 loop : -0.24 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.024 0.001 TYR A 188 PHE 0.017 0.001 PHE A 327 TRP 0.021 0.002 TRP A 248 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3140) covalent geometry : angle 0.53319 / 0.27 ( 4267) hydrogen bonds : bond 0.03603 / 2.40 ( 164) hydrogen bonds : angle 4.57535 / 3.15 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5376 (mmt) cc_final: 0.4857 (mmt) REVERT: A 100 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7287 (mmtt) REVERT: A 101 LEU cc_start: 0.8277 (mm) cc_final: 0.7860 (mm) REVERT: A 144 ASP cc_start: 0.8057 (t0) cc_final: 0.7697 (m-30) REVERT: A 233 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7515 (mm) REVERT: A 237 TYR cc_start: 0.8503 (t80) cc_final: 0.7526 (t80) REVERT: A 249 ARG cc_start: 0.6908 (ptm160) cc_final: 0.5235 (tpt-90) REVERT: A 320 MET cc_start: 0.7604 (mtt) cc_final: 0.6757 (ttt) REVERT: A 356 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7286 (ttp80) REVERT: A 359 MET cc_start: 0.7660 (ttt) cc_final: 0.7415 (ttm) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.0590 time to fit residues: 5.0864 Evaluate side-chains 72 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 248 TRP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 375 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: [30, 25, 31, 29, 34, 8, 15, 21, 3, 10, 27] chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 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 = 0.3741 r_free = 0.3741 target = 0.160195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120365 restraints weight = 3706.020| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.34 r_work: 0.3174 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3140 Z= 0.136 Angle : 0.545 6.432 4267 Z= 0.281 Chirality : 0.040 0.121 478 Planarity : 0.004 0.035 519 Dihedral : 5.266 41.743 499 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.06 % Allowed : 19.69 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.44), residues: 374 helix: 2.13 (0.35), residues: 206 sheet: -1.05 (0.80), residues: 47 loop : -0.27 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.024 0.001 TYR A 188 PHE 0.017 0.001 PHE A 327 TRP 0.022 0.002 TRP A 248 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 3140) covalent geometry : angle 0.54530 / 0.28 ( 4267) hydrogen bonds : bond 0.03730 / 2.48 ( 164) hydrogen bonds : angle 4.57217 / 3.16 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 996.50 seconds wall clock time: 17 minutes 45.37 seconds (1065.37 seconds total)