Starting phenix.real_space_refine on Wed Mar 5 20:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uwf_20922/03_2025/6uwf_20922.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwf_20922/03_2025/6uwf_20922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uwf_20922/03_2025/6uwf_20922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwf_20922/03_2025/6uwf_20922.map" model { file = "/net/cci-nas-00/data/ceres_data/6uwf_20922/03_2025/6uwf_20922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwf_20922/03_2025/6uwf_20922.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 18 5.16 5 C 2096 2.51 5 N 502 2.21 5 O 560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3178 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3105 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.06, per 1000 atoms: 0.96 Number of scatterers: 3178 At special positions: 0 Unit cell: (71.02, 67.84, 81.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 2 15.00 O 560 8.00 N 502 7.00 C 2096 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 449.7 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.650A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.883A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.982A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.589A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 107 removed outlier: 3.630A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.619A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.586A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.737A pdb=" N ARG A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.617A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.528A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 257 through 276 removed outlier: 5.780A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 295 through 307 removed outlier: 4.264A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.545A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.725A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.790A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.818A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 416 removed outlier: 4.063A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 672 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: 0.77 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 488 1.31 - 1.43: 788 1.43 - 1.56: 1894 1.56 - 1.68: 31 1.68 - 1.80: 35 Bond restraints: 3236 Sorted by residual: bond pdb=" C16 6OU A 502 " pdb=" O18 6OU A 502 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C16 6OU A 503 " pdb=" O18 6OU A 503 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C31 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C31 6OU A 503 " pdb=" O30 6OU A 503 " ideal model delta sigma weight residual 1.331 1.409 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C39 6OU A 502 " pdb=" C40 6OU A 502 " ideal model delta sigma weight residual 1.497 1.569 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 3231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 4295 3.07 - 6.14: 80 6.14 - 9.21: 15 9.21 - 12.28: 2 12.28 - 15.35: 2 Bond angle restraints: 4394 Sorted by residual: angle pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " pdb=" O26 6OU A 502 " ideal model delta sigma weight residual 93.95 109.30 -15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 108.18 -14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.48e+01 angle pdb=" N LEU A 374 " pdb=" CA LEU A 374 " pdb=" C LEU A 374 " ideal model delta sigma weight residual 113.17 108.81 4.36 1.26e+00 6.30e-01 1.20e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 119.66 -5.76 1.80e+00 3.09e-01 1.03e+01 ... (remaining 4389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 1842 28.42 - 56.85: 65 56.85 - 85.27: 10 85.27 - 113.70: 2 113.70 - 142.12: 3 Dihedral angle restraints: 1922 sinusoidal: 739 harmonic: 1183 Sorted by residual: dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N PHE A 122 " pdb=" CA PHE A 122 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" C37 6OU A 503 " pdb=" C38 6OU A 503 " pdb=" C39 6OU A 503 " pdb=" C40 6OU A 503 " ideal model delta sinusoidal sigma weight residual 178.01 -39.87 -142.12 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C09 6OU A 503 " pdb=" C10 6OU A 503 " pdb=" C11 6OU A 503 " pdb=" C12 6OU A 503 " ideal model delta sinusoidal sigma weight residual 179.71 -48.47 -131.82 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 1919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 368 0.046 - 0.092: 134 0.092 - 0.137: 29 0.137 - 0.183: 7 0.183 - 0.229: 3 Chirality restraints: 541 Sorted by residual: chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C20 6OU A 503 " pdb=" C19 6OU A 503 " pdb=" C21 6OU A 503 " pdb=" O30 6OU A 503 " both_signs ideal model delta sigma weight residual False 2.35 2.56 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL A 117 " pdb=" CA VAL A 117 " pdb=" CG1 VAL A 117 " pdb=" CG2 VAL A 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.82 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 538 not shown) Planarity restraints: 537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 45 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 153 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 206 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.030 5.00e-02 4.00e+02 ... (remaining 534 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 910 2.82 - 3.34: 3006 3.34 - 3.86: 5315 3.86 - 4.38: 6264 4.38 - 4.90: 10738 Nonbonded interactions: 26233 Sorted by model distance: nonbonded pdb=" O ALA A 360 " pdb=" OH TYR A 383 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.321 3.040 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.325 3.040 nonbonded pdb=" O THR A 340 " pdb=" OG1 THR A 344 " model vdw 2.336 3.040 nonbonded pdb=" O ALA A 348 " pdb=" OG1 THR A 352 " model vdw 2.345 3.040 ... (remaining 26228 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: 1.310 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.120 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 0.008 0.088 3236 Z= 0.508 Angle : 1.079 15.348 4394 Z= 0.513 Chirality : 0.049 0.229 541 Planarity : 0.008 0.054 537 Dihedral : 17.111 142.124 1172 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.32), residues: 413 helix: -2.35 (0.20), residues: 338 sheet: None (None), residues: 0 loop : -2.27 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 40 PHE 0.015 0.002 PHE A 157 TYR 0.029 0.003 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.323 Fit side-chains REVERT: A 327 ASN cc_start: 0.8784 (m110) cc_final: 0.8305 (m-40) REVERT: A 362 MET cc_start: 0.9011 (tpp) cc_final: 0.8494 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1077 time to fit residues: 7.0329 Evaluate side-chains 41 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.092543 restraints weight = 4322.693| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.59 r_work: 0.2817 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3236 Z= 0.216 Angle : 0.580 5.851 4394 Z= 0.292 Chirality : 0.039 0.149 541 Planarity : 0.005 0.033 537 Dihedral : 15.756 125.811 508 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.31 % Allowed : 10.46 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.39), residues: 413 helix: -0.45 (0.26), residues: 344 sheet: None (None), residues: 0 loop : -2.19 (0.68), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.009 0.001 PHE A 157 TYR 0.024 0.001 TYR A 299 ARG 0.003 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.331 Fit side-chains REVERT: A 327 ASN cc_start: 0.8908 (m110) cc_final: 0.8302 (m-40) REVERT: A 362 MET cc_start: 0.9313 (tpp) cc_final: 0.8769 (tpt) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.0930 time to fit residues: 5.8762 Evaluate side-chains 43 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.090912 restraints weight = 4237.171| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.66 r_work: 0.2713 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3236 Z= 0.250 Angle : 0.573 5.697 4394 Z= 0.286 Chirality : 0.040 0.144 541 Planarity : 0.004 0.029 537 Dihedral : 15.016 116.574 508 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.23 % Allowed : 10.46 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.41), residues: 413 helix: 0.49 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -2.45 (0.62), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 40 PHE 0.010 0.001 PHE A 157 TYR 0.020 0.001 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.348 Fit side-chains REVERT: A 61 ILE cc_start: 0.8837 (tt) cc_final: 0.8616 (tt) REVERT: A 219 GLU cc_start: 0.7887 (tt0) cc_final: 0.7547 (mt-10) REVERT: A 327 ASN cc_start: 0.8641 (m110) cc_final: 0.7998 (m-40) REVERT: A 362 MET cc_start: 0.9072 (tpp) cc_final: 0.8491 (tpt) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.0965 time to fit residues: 6.3435 Evaluate side-chains 46 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.089762 restraints weight = 4403.701| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.61 r_work: 0.2705 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3236 Z= 0.300 Angle : 0.597 5.431 4394 Z= 0.297 Chirality : 0.041 0.140 541 Planarity : 0.004 0.032 537 Dihedral : 14.748 111.722 508 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.54 % Allowed : 11.08 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.42), residues: 413 helix: 0.88 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -2.12 (0.64), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 40 PHE 0.011 0.001 PHE A 157 TYR 0.020 0.001 TYR A 299 ARG 0.004 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.336 Fit side-chains REVERT: A 327 ASN cc_start: 0.8734 (m110) cc_final: 0.8079 (m-40) REVERT: A 362 MET cc_start: 0.9159 (tpp) cc_final: 0.8616 (tpt) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.0966 time to fit residues: 5.8350 Evaluate side-chains 45 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 312 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090800 restraints weight = 4375.933| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.61 r_work: 0.2784 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3236 Z= 0.248 Angle : 0.567 5.669 4394 Z= 0.282 Chirality : 0.040 0.135 541 Planarity : 0.004 0.031 537 Dihedral : 14.467 108.899 508 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 13.23 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.42), residues: 413 helix: 1.16 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -2.00 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.018 0.001 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.347 Fit side-chains REVERT: A 219 GLU cc_start: 0.8011 (tt0) cc_final: 0.7724 (mt-10) REVERT: A 327 ASN cc_start: 0.8886 (m110) cc_final: 0.8278 (m-40) REVERT: A 362 MET cc_start: 0.9303 (tpp) cc_final: 0.8813 (tpt) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.0934 time to fit residues: 5.9540 Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090795 restraints weight = 4468.794| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.62 r_work: 0.2835 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3236 Z= 0.249 Angle : 0.566 6.101 4394 Z= 0.280 Chirality : 0.040 0.138 541 Planarity : 0.004 0.030 537 Dihedral : 13.986 104.382 508 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.15 % Allowed : 14.46 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 413 helix: 1.31 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.83 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.018 0.001 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.348 Fit side-chains REVERT: A 219 GLU cc_start: 0.7927 (tt0) cc_final: 0.7620 (mt-10) REVERT: A 327 ASN cc_start: 0.8879 (m110) cc_final: 0.8306 (m-40) REVERT: A 362 MET cc_start: 0.9310 (tpp) cc_final: 0.8829 (tpt) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1019 time to fit residues: 6.7040 Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091148 restraints weight = 4385.994| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.61 r_work: 0.2730 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3236 Z= 0.240 Angle : 0.564 6.521 4394 Z= 0.278 Chirality : 0.039 0.135 541 Planarity : 0.004 0.032 537 Dihedral : 13.120 98.199 508 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.15 % Allowed : 14.46 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.42), residues: 413 helix: 1.44 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.82 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.018 0.001 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.338 Fit side-chains REVERT: A 219 GLU cc_start: 0.7844 (tt0) cc_final: 0.7469 (mt-10) REVERT: A 327 ASN cc_start: 0.8705 (m110) cc_final: 0.8141 (m-40) REVERT: A 362 MET cc_start: 0.9143 (tpp) cc_final: 0.8635 (tpt) outliers start: 7 outliers final: 7 residues processed: 47 average time/residue: 0.0981 time to fit residues: 6.4801 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.0010 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094216 restraints weight = 4288.927| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.59 r_work: 0.2913 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3236 Z= 0.171 Angle : 0.539 8.188 4394 Z= 0.261 Chirality : 0.038 0.129 541 Planarity : 0.004 0.027 537 Dihedral : 12.407 88.267 508 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 14.46 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.43), residues: 413 helix: 1.57 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.52 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.009 0.001 PHE A 157 TYR 0.017 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.317 Fit side-chains REVERT: A 327 ASN cc_start: 0.8861 (m110) cc_final: 0.8393 (m-40) REVERT: A 362 MET cc_start: 0.9316 (tpp) cc_final: 0.9036 (mmm) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.0892 time to fit residues: 6.0112 Evaluate side-chains 46 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.091639 restraints weight = 4346.220| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.61 r_work: 0.2715 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3236 Z= 0.261 Angle : 0.593 9.034 4394 Z= 0.288 Chirality : 0.040 0.132 541 Planarity : 0.004 0.030 537 Dihedral : 12.388 90.495 508 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.46 % Allowed : 14.15 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.43), residues: 413 helix: 1.63 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.69 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.011 0.001 PHE A 157 TYR 0.018 0.001 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8715 (m110) cc_final: 0.8166 (m-40) REVERT: A 362 MET cc_start: 0.9140 (tpp) cc_final: 0.8620 (tpt) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.0913 time to fit residues: 6.1032 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 501 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.1980 chunk 7 optimal weight: 0.0670 chunk 13 optimal weight: 0.0870 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.0770 chunk 25 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 overall best weight: 0.1454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095788 restraints weight = 4218.245| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.59 r_work: 0.2930 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3236 Z= 0.134 Angle : 0.539 9.814 4394 Z= 0.258 Chirality : 0.038 0.130 541 Planarity : 0.004 0.029 537 Dihedral : 11.498 76.943 508 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.54 % Allowed : 15.08 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.43), residues: 413 helix: 1.74 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.36 (0.76), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 40 PHE 0.009 0.001 PHE A 157 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 61 ILE cc_start: 0.9018 (tt) cc_final: 0.8794 (tt) REVERT: A 327 ASN cc_start: 0.8805 (m110) cc_final: 0.8375 (m-40) REVERT: A 362 MET cc_start: 0.9322 (tpp) cc_final: 0.9013 (mmm) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.0961 time to fit residues: 6.0730 Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.092397 restraints weight = 4280.811| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.61 r_work: 0.2810 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3236 Z= 0.210 Angle : 0.569 10.055 4394 Z= 0.274 Chirality : 0.039 0.129 541 Planarity : 0.004 0.029 537 Dihedral : 11.539 80.228 508 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.54 % Allowed : 14.77 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.43), residues: 413 helix: 1.79 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.74 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.017 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.55 seconds wall clock time: 32 minutes 12.85 seconds (1932.85 seconds total)