Starting phenix.real_space_refine on Fri May 9 16:08:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrs_18625/05_2025/8qrs_18625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrs_18625/05_2025/8qrs_18625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrs_18625/05_2025/8qrs_18625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrs_18625/05_2025/8qrs_18625.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrs_18625/05_2025/8qrs_18625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrs_18625/05_2025/8qrs_18625.cif" } resolution = 2.86 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2034 2.51 5 N 504 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3093 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3083 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 16, 'TRANS': 398} Chain breaks: 2 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.86 Number of scatterers: 3093 At special positions: 0 Unit cell: (60.192, 69.388, 71.896, 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 15 16.00 O 540 8.00 N 504 7.00 C 2034 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: 0.89 Conformation dependent library (CDL) restraints added in 425.9 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 86.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 49 through 74 removed outlier: 3.591A pdb=" N VAL B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 118 Proline residue: B 83 - end of helix removed outlier: 3.589A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.501A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 155 through 158 removed outlier: 4.320A pdb=" N ALA B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.606A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 291 removed outlier: 3.677A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 319 removed outlier: 5.478A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.747A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.594A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.501A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) Proline residue: B 380 - end of helix removed outlier: 3.909A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.849A pdb=" N ILE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.824A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 209 256 hydrogen bonds defined for protein. 765 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: 0.83 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 978 1.34 - 1.46: 649 1.46 - 1.58: 1497 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3148 Sorted by residual: bond pdb=" N GLN B 601 " pdb=" CA GLN B 601 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N LEU B 49 " pdb=" CA LEU B 49 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" C LEU B 105 " pdb=" O LEU B 105 " ideal model delta sigma weight residual 1.238 1.245 -0.008 1.28e-02 6.10e+03 3.58e-01 bond pdb=" CA GLN B 154 " pdb=" C GLN B 154 " ideal model delta sigma weight residual 1.524 1.531 -0.008 1.26e-02 6.30e+03 3.56e-01 bond pdb=" C LEU B 379 " pdb=" O LEU B 379 " ideal model delta sigma weight residual 1.244 1.238 0.006 1.00e-02 1.00e+04 3.46e-01 ... (remaining 3143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 4028 0.90 - 1.80: 193 1.80 - 2.70: 44 2.70 - 3.59: 13 3.59 - 4.49: 10 Bond angle restraints: 4288 Sorted by residual: angle pdb=" C VAL B 222 " pdb=" N GLY B 223 " pdb=" CA GLY B 223 " ideal model delta sigma weight residual 122.66 120.59 2.07 9.80e-01 1.04e+00 4.48e+00 angle pdb=" N VAL B 72 " pdb=" CA VAL B 72 " pdb=" C VAL B 72 " ideal model delta sigma weight residual 111.00 109.08 1.92 1.09e+00 8.42e-01 3.10e+00 angle pdb=" N GLY B 223 " pdb=" CA GLY B 223 " pdb=" C GLY B 223 " ideal model delta sigma weight residual 111.12 114.01 -2.89 1.89e+00 2.80e-01 2.34e+00 angle pdb=" N VAL B 450 " pdb=" CA VAL B 450 " pdb=" CB VAL B 450 " ideal model delta sigma weight residual 112.07 109.81 2.26 1.52e+00 4.33e-01 2.21e+00 angle pdb=" C ASP B 294 " pdb=" N VAL B 295 " pdb=" CA VAL B 295 " ideal model delta sigma weight residual 120.56 122.41 -1.85 1.26e+00 6.30e-01 2.17e+00 ... (remaining 4283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.25: 1624 13.25 - 26.50: 158 26.50 - 39.74: 41 39.74 - 52.99: 16 52.99 - 66.24: 6 Dihedral angle restraints: 1845 sinusoidal: 674 harmonic: 1171 Sorted by residual: dihedral pdb=" CA SER B 73 " pdb=" C SER B 73 " pdb=" N GLY B 74 " pdb=" CA GLY B 74 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP B 388 " pdb=" CB ASP B 388 " pdb=" CG ASP B 388 " pdb=" OD1 ASP B 388 " ideal model delta sinusoidal sigma weight residual -30.00 -85.01 55.01 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -60.00 -118.31 58.31 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 361 0.026 - 0.053: 96 0.053 - 0.079: 59 0.079 - 0.106: 18 0.106 - 0.132: 4 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL B 222 " pdb=" N VAL B 222 " pdb=" C VAL B 222 " pdb=" CB VAL B 222 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 535 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 342 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO B 343 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 126 " -0.175 9.50e-02 1.11e+02 7.85e-02 3.99e+00 pdb=" NE ARG B 126 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 126 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 126 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 126 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " -0.137 9.50e-02 1.11e+02 6.18e-02 2.66e+00 pdb=" NE ARG B 335 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " -0.002 2.00e-02 2.50e+03 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 395 2.75 - 3.28: 3293 3.28 - 3.82: 5498 3.82 - 4.36: 6072 4.36 - 4.90: 10911 Nonbonded interactions: 26169 Sorted by model distance: nonbonded pdb=" OE1 GLN B 394 " pdb=" OG SER B 424 " model vdw 2.208 3.040 nonbonded pdb=" O THR B 350 " pdb=" OG SER B 351 " model vdw 2.236 3.040 nonbonded pdb=" O LEU B 318 " pdb=" OH TYR B 334 " model vdw 2.244 3.040 nonbonded pdb=" CD2 LEU B 284 " pdb=" CE LYS B 288 " model vdw 2.317 3.860 nonbonded pdb=" O THR B 416 " pdb=" OG1 THR B 420 " model vdw 2.369 3.040 ... (remaining 26164 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: 0.660 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3148 Z= 0.134 Angle : 0.531 4.493 4288 Z= 0.299 Chirality : 0.035 0.132 538 Planarity : 0.006 0.078 530 Dihedral : 12.975 66.238 1093 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.31 % Allowed : 11.62 % Favored : 88.07 % 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: 1.87 (0.43), residues: 409 helix: 1.59 (0.29), residues: 340 sheet: -1.52 (1.31), residues: 20 loop : 0.37 (0.94), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.002 0.001 HIS B 373 PHE 0.009 0.001 PHE B 299 TYR 0.007 0.001 TYR B 208 ARG 0.010 0.001 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.11412 ( 256) hydrogen bonds : angle 6.28012 ( 765) covalent geometry : bond 0.00261 ( 3148) covalent geometry : angle 0.53125 ( 4288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.348 Fit side-chains REVERT: B 85 ARG cc_start: 0.7368 (mtt180) cc_final: 0.5853 (tmt170) REVERT: B 247 LYS cc_start: 0.7660 (mttt) cc_final: 0.7204 (mtpm) REVERT: B 301 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7130 (ttt180) REVERT: B 362 LYS cc_start: 0.7990 (tttt) cc_final: 0.7669 (tttp) REVERT: B 407 GLN cc_start: 0.8182 (mt0) cc_final: 0.7976 (mp10) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 1.0729 time to fit residues: 54.3206 Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097679 restraints weight = 4015.439| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.03 r_work: 0.2995 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3148 Z= 0.128 Angle : 0.537 6.856 4288 Z= 0.264 Chirality : 0.037 0.136 538 Planarity : 0.005 0.042 530 Dihedral : 4.038 37.704 437 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.45 % Allowed : 11.31 % Favored : 86.24 % 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: 2.65 (0.42), residues: 409 helix: 2.26 (0.28), residues: 338 sheet: -1.78 (1.29), residues: 20 loop : -0.13 (0.92), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 PHE 0.011 0.001 PHE B 336 TYR 0.007 0.001 TYR B 208 ARG 0.005 0.001 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 256) hydrogen bonds : angle 4.59131 ( 765) covalent geometry : bond 0.00284 ( 3148) covalent geometry : angle 0.53707 ( 4288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.339 Fit side-chains REVERT: B 85 ARG cc_start: 0.7349 (mtt180) cc_final: 0.5704 (tmt170) REVERT: B 247 LYS cc_start: 0.7751 (mttt) cc_final: 0.7338 (mtpm) REVERT: B 301 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7121 (ttt180) REVERT: B 362 LYS cc_start: 0.8014 (tttt) cc_final: 0.7694 (tttp) REVERT: B 387 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7265 (mtt) REVERT: B 407 GLN cc_start: 0.8189 (mt0) cc_final: 0.7884 (mp10) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.9541 time to fit residues: 47.5270 Evaluate side-chains 42 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097133 restraints weight = 4051.469| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.05 r_work: 0.2996 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3148 Z= 0.137 Angle : 0.521 6.766 4288 Z= 0.256 Chirality : 0.037 0.144 538 Planarity : 0.004 0.034 530 Dihedral : 4.120 41.037 437 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.98 % Allowed : 11.62 % Favored : 84.40 % 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: 2.99 (0.43), residues: 409 helix: 2.38 (0.28), residues: 338 sheet: -1.75 (1.25), residues: 20 loop : 0.90 (1.03), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 461 HIS 0.001 0.001 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.006 0.001 TYR B 276 ARG 0.005 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 256) hydrogen bonds : angle 4.49164 ( 765) covalent geometry : bond 0.00321 ( 3148) covalent geometry : angle 0.52141 ( 4288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.343 Fit side-chains REVERT: B 85 ARG cc_start: 0.7443 (mtt180) cc_final: 0.5787 (tmt170) REVERT: B 247 LYS cc_start: 0.7802 (mttt) cc_final: 0.7393 (mtpm) REVERT: B 301 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7153 (ttt180) REVERT: B 362 LYS cc_start: 0.8058 (tttt) cc_final: 0.7756 (tttp) REVERT: B 387 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7329 (mtt) REVERT: B 407 GLN cc_start: 0.8189 (mt0) cc_final: 0.7906 (mt0) outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 1.0244 time to fit residues: 49.8955 Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097307 restraints weight = 4136.190| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.07 r_work: 0.3002 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3148 Z= 0.132 Angle : 0.511 7.029 4288 Z= 0.248 Chirality : 0.037 0.145 538 Planarity : 0.004 0.032 530 Dihedral : 4.158 46.703 437 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.28 % Allowed : 12.23 % Favored : 83.49 % 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: 3.08 (0.42), residues: 409 helix: 2.45 (0.28), residues: 338 sheet: -1.57 (1.26), residues: 20 loop : 0.82 (0.96), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 338 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.005 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 256) hydrogen bonds : angle 4.37980 ( 765) covalent geometry : bond 0.00308 ( 3148) covalent geometry : angle 0.51121 ( 4288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8194 (tt) cc_final: 0.7976 (tm) REVERT: B 85 ARG cc_start: 0.7350 (mtt180) cc_final: 0.5576 (tmt170) REVERT: B 247 LYS cc_start: 0.7755 (mttt) cc_final: 0.7342 (mtpm) REVERT: B 267 MET cc_start: 0.8177 (mmm) cc_final: 0.7924 (mtt) REVERT: B 301 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7141 (ttt180) REVERT: B 362 LYS cc_start: 0.7992 (tttt) cc_final: 0.7700 (tttp) REVERT: B 387 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7257 (mtt) REVERT: B 407 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: B 446 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7218 (m) REVERT: B 475 ASP cc_start: 0.7197 (m-30) cc_final: 0.6980 (m-30) outliers start: 14 outliers final: 7 residues processed: 49 average time/residue: 0.9835 time to fit residues: 49.8939 Evaluate side-chains 51 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096893 restraints weight = 4081.579| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.06 r_work: 0.2990 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3148 Z= 0.137 Angle : 0.511 7.223 4288 Z= 0.249 Chirality : 0.037 0.146 538 Planarity : 0.004 0.034 530 Dihedral : 4.402 55.220 437 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.59 % Allowed : 14.07 % Favored : 81.35 % 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: 3.02 (0.42), residues: 409 helix: 2.44 (0.28), residues: 338 sheet: -1.72 (1.23), residues: 20 loop : 0.60 (0.91), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.002 0.001 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.007 0.001 TYR B 334 ARG 0.003 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 256) hydrogen bonds : angle 4.37804 ( 765) covalent geometry : bond 0.00324 ( 3148) covalent geometry : angle 0.51078 ( 4288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7817 (mttt) cc_final: 0.7415 (mtpm) REVERT: B 301 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7177 (ttt180) REVERT: B 362 LYS cc_start: 0.8044 (tttt) cc_final: 0.7751 (tttp) REVERT: B 387 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7396 (mtt) REVERT: B 407 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: B 446 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7239 (m) outliers start: 15 outliers final: 7 residues processed: 45 average time/residue: 1.0112 time to fit residues: 47.1521 Evaluate side-chains 49 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 403 GLN B 447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098130 restraints weight = 4150.727| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.10 r_work: 0.3005 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3148 Z= 0.124 Angle : 0.512 8.298 4288 Z= 0.244 Chirality : 0.036 0.144 538 Planarity : 0.004 0.035 530 Dihedral : 4.465 59.429 437 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.59 % Allowed : 14.07 % Favored : 81.35 % 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: 3.07 (0.42), residues: 409 helix: 2.50 (0.28), residues: 338 sheet: -1.63 (1.24), residues: 20 loop : 0.40 (0.87), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.003 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 256) hydrogen bonds : angle 4.30710 ( 765) covalent geometry : bond 0.00287 ( 3148) covalent geometry : angle 0.51248 ( 4288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7791 (mttt) cc_final: 0.7387 (mtpm) REVERT: B 292 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6987 (ptp) REVERT: B 301 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7171 (ttt180) REVERT: B 362 LYS cc_start: 0.7984 (tttt) cc_final: 0.7699 (tttp) REVERT: B 387 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7333 (mtt) REVERT: B 407 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: B 446 VAL cc_start: 0.7450 (OUTLIER) cc_final: 0.7182 (m) REVERT: B 475 ASP cc_start: 0.7164 (m-30) cc_final: 0.6939 (m-30) outliers start: 15 outliers final: 5 residues processed: 49 average time/residue: 0.9742 time to fit residues: 49.4408 Evaluate side-chains 50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096921 restraints weight = 4070.835| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.06 r_work: 0.2992 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3148 Z= 0.144 Angle : 0.528 8.663 4288 Z= 0.253 Chirality : 0.038 0.144 538 Planarity : 0.004 0.034 530 Dihedral : 4.338 54.276 437 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.06 % Allowed : 16.21 % Favored : 80.73 % 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: 3.01 (0.42), residues: 409 helix: 2.45 (0.28), residues: 338 sheet: -1.62 (1.24), residues: 20 loop : 0.45 (0.87), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.002 0.001 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 256) hydrogen bonds : angle 4.34075 ( 765) covalent geometry : bond 0.00344 ( 3148) covalent geometry : angle 0.52845 ( 4288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7803 (mttt) cc_final: 0.7403 (mtpm) REVERT: B 292 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7033 (ptp) REVERT: B 301 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7204 (ttt180) REVERT: B 362 LYS cc_start: 0.7998 (tttt) cc_final: 0.7708 (tttp) REVERT: B 387 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7376 (mtt) REVERT: B 407 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: B 446 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7246 (m) REVERT: B 454 SER cc_start: 0.8355 (m) cc_final: 0.8064 (p) outliers start: 10 outliers final: 3 residues processed: 45 average time/residue: 1.0627 time to fit residues: 49.4855 Evaluate side-chains 48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.097736 restraints weight = 4090.450| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.07 r_work: 0.2995 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3148 Z= 0.132 Angle : 0.522 8.198 4288 Z= 0.249 Chirality : 0.037 0.143 538 Planarity : 0.004 0.034 530 Dihedral : 3.464 11.890 435 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.75 % Allowed : 16.51 % Favored : 80.73 % 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: 3.04 (0.42), residues: 409 helix: 2.47 (0.28), residues: 338 sheet: -1.61 (1.25), residues: 20 loop : 0.43 (0.87), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.007 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 256) hydrogen bonds : angle 4.29320 ( 765) covalent geometry : bond 0.00311 ( 3148) covalent geometry : angle 0.52177 ( 4288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7795 (mttt) cc_final: 0.7393 (mtpm) REVERT: B 292 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7032 (ptp) REVERT: B 301 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7194 (ttt180) REVERT: B 362 LYS cc_start: 0.7976 (tttt) cc_final: 0.7689 (tttp) REVERT: B 387 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7339 (mtt) REVERT: B 407 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: B 446 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7202 (m) outliers start: 9 outliers final: 2 residues processed: 45 average time/residue: 1.0736 time to fit residues: 49.9917 Evaluate side-chains 47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099905 restraints weight = 4078.996| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.07 r_work: 0.3035 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3148 Z= 0.113 Angle : 0.512 8.239 4288 Z= 0.243 Chirality : 0.036 0.137 538 Planarity : 0.004 0.034 530 Dihedral : 3.436 11.817 435 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.83 % Allowed : 16.82 % Favored : 81.35 % 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: 3.17 (0.42), residues: 409 helix: 2.50 (0.28), residues: 341 sheet: -1.60 (1.26), residues: 20 loop : 0.89 (0.86), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 PHE 0.007 0.001 PHE B 237 TYR 0.006 0.001 TYR B 208 ARG 0.004 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 256) hydrogen bonds : angle 4.23085 ( 765) covalent geometry : bond 0.00254 ( 3148) covalent geometry : angle 0.51195 ( 4288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7782 (mttt) cc_final: 0.7376 (mtpm) REVERT: B 292 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7006 (ptp) REVERT: B 301 ARG cc_start: 0.7988 (ttm170) cc_final: 0.7203 (ttt180) REVERT: B 362 LYS cc_start: 0.7954 (tttt) cc_final: 0.7693 (tttp) REVERT: B 387 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7309 (mtt) REVERT: B 407 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: B 446 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7102 (m) outliers start: 6 outliers final: 1 residues processed: 44 average time/residue: 1.1141 time to fit residues: 50.6344 Evaluate side-chains 45 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093100 restraints weight = 4049.369| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.15 r_work: 0.2918 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3148 Z= 0.143 Angle : 0.529 8.213 4288 Z= 0.253 Chirality : 0.038 0.144 538 Planarity : 0.004 0.035 530 Dihedral : 3.493 11.700 435 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.83 % Allowed : 17.13 % Favored : 81.04 % 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: 3.12 (0.41), residues: 409 helix: 2.46 (0.27), residues: 341 sheet: -1.65 (1.24), residues: 20 loop : 0.89 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.002 0.001 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 256) hydrogen bonds : angle 4.29509 ( 765) covalent geometry : bond 0.00344 ( 3148) covalent geometry : angle 0.52863 ( 4288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7609 (mttt) cc_final: 0.7211 (mtpm) REVERT: B 292 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6929 (ptp) REVERT: B 301 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7112 (ttt180) REVERT: B 362 LYS cc_start: 0.7760 (tttt) cc_final: 0.7488 (tttp) REVERT: B 387 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: B 407 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: B 446 VAL cc_start: 0.7342 (OUTLIER) cc_final: 0.7061 (m) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 1.0318 time to fit residues: 45.9312 Evaluate side-chains 45 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094352 restraints weight = 4072.527| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.13 r_work: 0.2941 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.124 Angle : 0.516 8.229 4288 Z= 0.246 Chirality : 0.037 0.142 538 Planarity : 0.004 0.035 530 Dihedral : 3.483 11.617 435 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.45 % Allowed : 16.51 % Favored : 81.04 % 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: 3.16 (0.41), residues: 409 helix: 2.49 (0.28), residues: 341 sheet: -1.55 (1.24), residues: 20 loop : 0.86 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.007 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 256) hydrogen bonds : angle 4.27083 ( 765) covalent geometry : bond 0.00291 ( 3148) covalent geometry : angle 0.51589 ( 4288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.73 seconds wall clock time: 43 minutes 9.35 seconds (2589.35 seconds total)