Starting phenix.real_space_refine on Wed Mar 5 17:25:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrs_18625/03_2025/8qrs_18625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrs_18625/03_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_18625/03_2025/8qrs_18625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrs_18625/03_2025/8qrs_18625.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrs_18625/03_2025/8qrs_18625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrs_18625/03_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-5624/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: 2.63, per 1000 atoms: 0.85 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: 0.84 Conformation dependent library (CDL) restraints added in 464.0 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: 0.28 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: 0.87 Time building geometry restraints manager: 1.00 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: 0.560 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.780 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- 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= 0.169 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 *********************** 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 : 0.341 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: 1.0770 time to fit residues: 54.5398 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 : 0.357 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.131539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098183 restraints weight = 4011.889| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.04 r_work: 0.3000 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1331 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= 0.188 Angle : 0.538 6.908 4288 Z= 0.263 Chirality : 0.037 0.139 538 Planarity : 0.005 0.042 530 Dihedral : 4.041 38.154 437 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.36 % Allowed : 10.40 % 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: 2.79 (0.42), residues: 409 helix: 2.32 (0.28), residues: 337 sheet: -1.76 (1.30), residues: 20 loop : 0.22 (0.98), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 461 HIS 0.001 0.001 HIS B 452 PHE 0.011 0.001 PHE B 336 TYR 0.007 0.001 TYR B 208 ARG 0.004 0.001 ARG B 126 *********************** 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 60 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.317 Fit side-chains REVERT: B 85 ARG cc_start: 0.7404 (mtt180) cc_final: 0.5761 (tmt170) REVERT: B 247 LYS cc_start: 0.7728 (mttt) cc_final: 0.7313 (mtpm) REVERT: B 301 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7139 (ttt180) REVERT: B 387 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7344 (mtt) REVERT: B 407 GLN cc_start: 0.8216 (mt0) cc_final: 0.7912 (mp10) outliers start: 11 outliers final: 2 residues processed: 54 average time/residue: 1.0180 time to fit residues: 57.0024 Evaluate side-chains 43 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.131381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098245 restraints weight = 4035.552| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.04 r_work: 0.3010 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3148 Z= 0.189 Angle : 0.509 6.863 4288 Z= 0.248 Chirality : 0.037 0.144 538 Planarity : 0.004 0.034 530 Dihedral : 4.098 41.101 437 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.67 % Allowed : 12.54 % Favored : 83.79 % 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: 3.05 (0.43), residues: 409 helix: 2.43 (0.28), residues: 338 sheet: -1.79 (1.26), residues: 20 loop : 0.96 (1.03), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 PHE 0.009 0.001 PHE B 237 TYR 0.005 0.001 TYR B 276 ARG 0.006 0.001 ARG B 335 *********************** 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: 12 poor density : 42 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 85 ARG cc_start: 0.7365 (mtt180) cc_final: 0.5614 (tmt170) REVERT: B 247 LYS cc_start: 0.7742 (mttt) cc_final: 0.7326 (mtpm) REVERT: B 301 ARG cc_start: 0.7979 (ttm110) cc_final: 0.7095 (ttt180) REVERT: B 331 LYS cc_start: 0.8231 (mtmt) cc_final: 0.8027 (mtmt) REVERT: B 362 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7694 (tttp) REVERT: B 387 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7282 (mtt) REVERT: B 407 GLN cc_start: 0.8168 (mt0) cc_final: 0.7879 (mt0) outliers start: 12 outliers final: 6 residues processed: 46 average time/residue: 1.0233 time to fit residues: 48.8089 Evaluate side-chains 47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 388 ASP 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: 0.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.130366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096839 restraints weight = 4121.613| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.07 r_work: 0.2985 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1721 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= 0.210 Angle : 0.512 6.996 4288 Z= 0.249 Chirality : 0.037 0.145 538 Planarity : 0.004 0.032 530 Dihedral : 4.162 47.284 437 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.28 % Allowed : 12.54 % Favored : 83.18 % 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: 3.06 (0.42), residues: 409 helix: 2.45 (0.28), residues: 338 sheet: -1.71 (1.24), residues: 20 loop : 0.79 (0.97), 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 0.010 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 *********************** 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 56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 85 ARG cc_start: 0.7393 (mtt180) cc_final: 0.5618 (tmt170) REVERT: B 247 LYS cc_start: 0.7789 (mttt) cc_final: 0.7379 (mtpm) REVERT: B 267 MET cc_start: 0.8289 (mmm) cc_final: 0.8010 (mtt) REVERT: B 301 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7150 (ttt180) REVERT: B 362 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7746 (tttp) REVERT: B 387 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7332 (mtt) REVERT: B 407 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: B 446 VAL cc_start: 0.7523 (OUTLIER) cc_final: 0.7260 (m) outliers start: 14 outliers final: 7 residues processed: 47 average time/residue: 1.0779 time to fit residues: 52.3093 Evaluate side-chains 53 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 132 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 362 LYS 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: 3.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.131299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097985 restraints weight = 4079.410| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.06 r_work: 0.3014 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1817 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= 0.183 Angle : 0.506 7.892 4288 Z= 0.242 Chirality : 0.036 0.141 538 Planarity : 0.004 0.034 530 Dihedral : 4.348 54.977 437 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.98 % Allowed : 14.37 % Favored : 81.65 % 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: 3.11 (0.42), residues: 409 helix: 2.50 (0.28), residues: 338 sheet: -1.73 (1.23), residues: 20 loop : 0.67 (0.94), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.005 0.001 TYR B 334 ARG 0.003 0.000 ARG B 335 *********************** 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 53 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7778 (mttt) cc_final: 0.7372 (mtpm) REVERT: B 267 MET cc_start: 0.8222 (mmm) cc_final: 0.7931 (mtt) REVERT: B 301 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7155 (ttt180) REVERT: B 362 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7714 (tttp) REVERT: B 387 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7318 (mtt) REVERT: B 407 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: B 446 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7197 (m) outliers start: 13 outliers final: 3 residues processed: 45 average time/residue: 0.9854 time to fit residues: 46.0354 Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 362 LYS 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: 0.6980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.130278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096738 restraints weight = 4153.121| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.08 r_work: 0.2988 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 0.032 3148 Z= 0.210 Angle : 0.519 7.882 4288 Z= 0.249 Chirality : 0.037 0.144 538 Planarity : 0.004 0.034 530 Dihedral : 4.440 58.310 437 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.28 % Allowed : 14.68 % 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: 3.06 (0.42), residues: 409 helix: 2.49 (0.28), residues: 338 sheet: -1.74 (1.23), residues: 20 loop : 0.49 (0.89), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 338 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 0.004 0.000 ARG B 335 *********************** 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 56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7821 (mttt) cc_final: 0.7420 (mtpm) REVERT: B 267 MET cc_start: 0.8274 (mmm) cc_final: 0.8045 (mtt) REVERT: B 292 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7041 (ptp) REVERT: B 301 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7210 (ttt180) REVERT: B 362 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7732 (tttp) REVERT: B 387 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7407 (mtt) REVERT: B 407 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: B 446 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7211 (m) outliers start: 14 outliers final: 5 residues processed: 47 average time/residue: 1.0022 time to fit residues: 48.7838 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 : 0.310 ------------------------------------------------------------------------------- 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 362 LYS 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: 0.7980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.129062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095532 restraints weight = 4074.441| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.05 r_work: 0.2970 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.004 0.034 3148 Z= 0.254 Angle : 0.536 8.454 4288 Z= 0.259 Chirality : 0.038 0.145 538 Planarity : 0.004 0.034 530 Dihedral : 4.363 53.959 437 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.98 % Allowed : 14.98 % 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: 3.00 (0.42), residues: 409 helix: 2.45 (0.28), residues: 338 sheet: -1.73 (1.22), residues: 20 loop : 0.44 (0.88), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.002 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 *********************** 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 56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7827 (mttt) cc_final: 0.7426 (mtpm) REVERT: B 292 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7133 (ptp) REVERT: B 301 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7164 (ttt180) REVERT: B 362 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7752 (tttp) REVERT: B 387 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7406 (mtt) REVERT: B 407 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: B 446 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7269 (m) REVERT: B 454 SER cc_start: 0.8387 (m) cc_final: 0.8094 (p) outliers start: 13 outliers final: 4 residues processed: 48 average time/residue: 1.0112 time to fit residues: 50.3080 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 : 0.309 ------------------------------------------------------------------------------- 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 362 LYS 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 450 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: 0.6980 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.131561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098096 restraints weight = 4080.833| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.08 r_work: 0.3001 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1963 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= 0.193 Angle : 0.519 8.149 4288 Z= 0.248 Chirality : 0.037 0.144 538 Planarity : 0.004 0.033 530 Dihedral : 3.499 11.816 435 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.06 % Allowed : 15.90 % 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: 3.04 (0.42), residues: 409 helix: 2.49 (0.28), residues: 338 sheet: -1.65 (1.25), residues: 20 loop : 0.34 (0.87), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 PHE 0.008 0.001 PHE B 237 TYR 0.007 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 *********************** 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 54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7779 (mttt) cc_final: 0.7379 (mtpm) REVERT: B 292 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7044 (ptp) REVERT: B 301 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7160 (ttt180) REVERT: B 362 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7661 (tttp) REVERT: B 387 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7339 (mtt) REVERT: B 407 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: B 446 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7206 (m) outliers start: 10 outliers final: 2 residues processed: 48 average time/residue: 1.0520 time to fit residues: 52.4054 Evaluate side-chains 47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 362 LYS 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 450 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.0270 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.0030 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.4248 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.130448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.096743 restraints weight = 4038.535| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.10 r_work: 0.2980 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3148 Z= 0.166 Angle : 0.509 8.262 4288 Z= 0.241 Chirality : 0.037 0.140 538 Planarity : 0.004 0.034 530 Dihedral : 3.408 11.900 435 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.67 % Allowed : 15.60 % 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: 3.24 (0.41), residues: 409 helix: 2.56 (0.27), residues: 341 sheet: -1.58 (1.27), residues: 20 loop : 0.83 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 PHE 0.008 0.001 PHE B 237 TYR 0.005 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 *********************** 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 53 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7653 (mttt) cc_final: 0.7240 (mtpm) REVERT: B 301 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7118 (ttt180) REVERT: B 362 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7496 (tttp) REVERT: B 387 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7118 (mtt) REVERT: B 407 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: B 446 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.6949 (m) outliers start: 12 outliers final: 3 residues processed: 46 average time/residue: 1.0270 time to fit residues: 49.0426 Evaluate side-chains 47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 362 LYS 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 450 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.131408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097579 restraints weight = 4016.465| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.09 r_work: 0.2989 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2221 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= 0.197 Angle : 0.526 8.117 4288 Z= 0.249 Chirality : 0.037 0.141 538 Planarity : 0.004 0.035 530 Dihedral : 3.448 11.463 435 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.14 % Allowed : 18.04 % Favored : 79.82 % 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: 3.22 (0.41), residues: 409 helix: 2.54 (0.27), residues: 341 sheet: -1.60 (1.26), residues: 20 loop : 0.84 (0.88), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.004 0.000 ARG B 335 ********************** 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: 7 poor density : 39 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7657 (mttt) cc_final: 0.7248 (mtpm) REVERT: B 301 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7163 (ttt180) REVERT: B 362 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7556 (tttp) REVERT: B 387 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7210 (mtt) REVERT: B 407 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: B 446 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6982 (m) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 1.0798 time to fit residues: 45.8149 Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 362 LYS 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 450 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.128700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094360 restraints weight = 4048.039| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.13 r_work: 0.2939 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2194 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= 0.195 Angle : 0.525 8.563 4288 Z= 0.248 Chirality : 0.037 0.141 538 Planarity : 0.004 0.035 530 Dihedral : 3.420 11.296 435 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 3.25 (0.41), residues: 409 helix: 2.57 (0.27), residues: 341 sheet: -1.55 (1.25), residues: 20 loop : 0.81 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2361.09 seconds wall clock time: 41 minutes 1.97 seconds (2461.97 seconds total)