Starting phenix.real_space_refine on Tue Aug 4 14:19:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j04_61048/08_2026/9j04_61048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j04_61048/08_2026/9j04_61048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j04_61048/08_2026/9j04_61048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j04_61048/08_2026/9j04_61048.map" model { file = "/net/cci-nas-00/data/ceres_data/9j04_61048/08_2026/9j04_61048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j04_61048/08_2026/9j04_61048.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 30 5.16 5 C 2450 2.51 5 N 639 2.21 5 O 662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3782 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3764 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 26, 'TRANS': 461} Chain breaks: 3 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'L8P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.28 Number of scatterers: 3782 At special positions: 0 Unit cell: (102, 58.65, 76.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 1 15.00 O 662 8.00 N 639 7.00 C 2450 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: 0.30 Conformation dependent library (CDL) restraints added in 145.2 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 67.6% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 14 through 26 removed outlier: 4.806A pdb=" N THR A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 131 through 155 removed outlier: 4.585A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.700A pdb=" N LEU A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 211 removed outlier: 3.621A pdb=" N TYR A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.640A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.765A pdb=" N TYR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.604A pdb=" N HIS A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.050A pdb=" N THR A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 332 through 357 removed outlier: 3.905A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 removed outlier: 4.382A pdb=" N VAL A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.567A pdb=" N ILE A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 424 through 449 removed outlier: 3.979A pdb=" N LEU A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.794A pdb=" N GLY A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Proline residue: A 473 - end of helix removed outlier: 3.712A pdb=" N SER A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.669A pdb=" N GLU A 480 " --> pdb=" O MET A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 removed outlier: 3.633A pdb=" N VAL A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.824A pdb=" N LEU A 504 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.714A pdb=" N HIS A 48 " --> pdb=" O ILE A 110 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 546 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: 0.52 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 580 1.32 - 1.45: 1128 1.45 - 1.59: 2114 1.59 - 1.72: 0 1.72 - 1.86: 48 Bond restraints: 3870 Sorted by residual: bond pdb=" C5 L8P A 601 " pdb=" C6 L8P A 601 " ideal model delta sigma weight residual 1.348 1.490 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C2 L8P A 601 " pdb=" N3 L8P A 601 " ideal model delta sigma weight residual 1.349 1.486 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C4 L8P A 601 " pdb=" N3 L8P A 601 " ideal model delta sigma weight residual 1.316 1.448 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C4 L8P A 601 " pdb=" N4 L8P A 601 " ideal model delta sigma weight residual 1.343 1.451 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C6 L8P A 601 " pdb=" N1 L8P A 601 " ideal model delta sigma weight residual 1.349 1.455 -0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 3865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 5165 1.89 - 3.78: 84 3.78 - 5.66: 16 5.66 - 7.55: 1 7.55 - 9.44: 2 Bond angle restraints: 5268 Sorted by residual: angle pdb=" N ILE A 373 " pdb=" CA ILE A 373 " pdb=" C ILE A 373 " ideal model delta sigma weight residual 112.96 108.38 4.58 1.00e+00 1.00e+00 2.09e+01 angle pdb=" C VAL A 127 " pdb=" N CYS A 128 " pdb=" CA CYS A 128 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" O4' L8P A 601 " pdb=" C4' L8P A 601 " pdb=" P L8P A 601 " ideal model delta sigma weight residual 116.17 106.73 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 111.62 109.22 2.40 7.90e-01 1.60e+00 9.22e+00 angle pdb=" C4' L8P A 601 " pdb=" P L8P A 601 " pdb=" OP1 L8P A 601 " ideal model delta sigma weight residual 101.44 109.44 -8.00 3.00e+00 1.11e-01 7.11e+00 ... (remaining 5263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 1993 14.58 - 29.15: 232 29.15 - 43.73: 45 43.73 - 58.31: 8 58.31 - 72.88: 6 Dihedral angle restraints: 2284 sinusoidal: 880 harmonic: 1404 Sorted by residual: dihedral pdb=" CA VAL A 127 " pdb=" C VAL A 127 " pdb=" N CYS A 128 " pdb=" CA CYS A 128 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR A 354 " pdb=" C TYR A 354 " pdb=" N GLY A 355 " pdb=" CA GLY A 355 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 466 " pdb=" C ARG A 466 " pdb=" N VAL A 467 " pdb=" CA VAL A 467 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.09e+00 ... (remaining 2281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 316 0.027 - 0.054: 187 0.054 - 0.081: 69 0.081 - 0.109: 34 0.109 - 0.136: 8 Chirality restraints: 614 Sorted by residual: chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" C2' L8P A 601 " pdb=" C1' L8P A 601 " pdb=" C3' L8P A 601 " pdb=" O4' L8P A 601 " both_signs ideal model delta sigma weight residual False -2.39 -2.52 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ASP A 359 " pdb=" N ASP A 359 " pdb=" C ASP A 359 " pdb=" CB ASP A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 611 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A 27 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 244 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 245 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 449 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 450 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " -0.021 5.00e-02 4.00e+02 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1343 2.86 - 3.37: 3566 3.37 - 3.88: 5762 3.88 - 4.39: 6611 4.39 - 4.90: 11233 Nonbonded interactions: 28515 Sorted by model distance: nonbonded pdb=" O SER A 265 " pdb=" OG SER A 265 " model vdw 2.350 3.040 nonbonded pdb=" O SER A 255 " pdb=" OG SER A 255 " model vdw 2.351 3.040 nonbonded pdb=" NH1 ARG A 80 " pdb=" OD2 ASP A 107 " model vdw 2.352 3.120 nonbonded pdb=" NH2 ARG A 131 " pdb=" OE1 GLU A 480 " model vdw 2.391 3.120 nonbonded pdb=" NE ARG A 69 " pdb=" O GLY A 73 " model vdw 2.432 3.120 ... (remaining 28510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.010 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.020 Find NCS groups from input model: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.006 0.142 3870 Z= 0.292 Angle : 0.655 9.438 5268 Z= 0.351 Chirality : 0.042 0.136 614 Planarity : 0.005 0.054 659 Dihedral : 13.043 72.883 1380 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.34), residues: 480 helix: -1.91 (0.25), residues: 323 sheet: None (None), residues: 0 loop : -2.77 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.014 0.002 TYR A 264 PHE 0.017 0.001 PHE A 438 TRP 0.014 0.001 TRP A 346 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.29 ( 3870) covalent geometry : angle 0.65510 / 0.35 ( 5268) hydrogen bonds : bond 0.14709 / 10.32 ( 184) hydrogen bonds : angle 5.22993 / 3.70 ( 546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.090 Fit side-chains REVERT: A 107 ASP cc_start: 0.7928 (m-30) cc_final: 0.7492 (m-30) REVERT: A 142 MET cc_start: 0.8189 (mmt) cc_final: 0.6677 (mmt) REVERT: A 369 LEU cc_start: 0.8499 (tp) cc_final: 0.8203 (tp) REVERT: A 455 GLN cc_start: 0.8498 (mm110) cc_final: 0.7443 (pm20) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0737 time to fit residues: 8.2404 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 398 GLN A 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101941 restraints weight = 4472.637| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.87 r_work: 0.3160 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3870 Z= 0.138 Angle : 0.599 8.686 5268 Z= 0.299 Chirality : 0.042 0.218 614 Planarity : 0.005 0.045 659 Dihedral : 5.060 57.550 535 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.98 % Allowed : 11.36 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.38), residues: 480 helix: -0.75 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.15 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.011 0.001 TYR A 169 PHE 0.013 0.001 PHE A 351 TRP 0.015 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3870) covalent geometry : angle 0.59858 / 0.30 ( 5268) hydrogen bonds : bond 0.04952 / 3.23 ( 184) hydrogen bonds : angle 4.07621 / 2.77 ( 546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.151 Fit side-chains REVERT: A 286 ARG cc_start: 0.9140 (tpp80) cc_final: 0.8928 (tpp80) REVERT: A 336 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7352 (ptp90) REVERT: A 369 LEU cc_start: 0.8398 (tp) cc_final: 0.8165 (tp) REVERT: A 417 GLN cc_start: 0.8215 (mt0) cc_final: 0.7814 (mp10) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.0754 time to fit residues: 6.7397 Evaluate side-chains 79 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 17 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.2469 > 50:) chunk 15 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.102640 restraints weight = 4331.165| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.76 r_work: 0.3201 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3870 Z= 0.109 Angle : 0.543 7.432 5268 Z= 0.271 Chirality : 0.040 0.227 614 Planarity : 0.004 0.042 659 Dihedral : 4.765 55.877 535 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.47 % Allowed : 11.85 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.39), residues: 480 helix: -0.16 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.71 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.018 0.001 TYR A 264 PHE 0.009 0.001 PHE A 351 TRP 0.013 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 3870) covalent geometry : angle 0.54271 / 0.27 ( 5268) hydrogen bonds : bond 0.03988 / 2.58 ( 184) hydrogen bonds : angle 3.79681 / 2.58 ( 546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.085 Fit side-chains REVERT: A 69 ARG cc_start: 0.8273 (ptp90) cc_final: 0.7990 (ttm110) REVERT: A 107 ASP cc_start: 0.8062 (m-30) cc_final: 0.7746 (m-30) REVERT: A 112 ASP cc_start: 0.8669 (t0) cc_final: 0.8379 (t0) REVERT: A 142 MET cc_start: 0.8308 (mmt) cc_final: 0.6861 (mmt) REVERT: A 286 ARG cc_start: 0.9188 (tpp80) cc_final: 0.8952 (tpp80) REVERT: A 310 ARG cc_start: 0.8341 (mtt180) cc_final: 0.8095 (mtt-85) REVERT: A 349 THR cc_start: 0.7719 (m) cc_final: 0.7474 (m) REVERT: A 369 LEU cc_start: 0.8436 (tp) cc_final: 0.8202 (tp) REVERT: A 417 GLN cc_start: 0.8153 (mt0) cc_final: 0.7767 (mp10) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.0703 time to fit residues: 6.9711 Evaluate side-chains 77 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 46 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102848 restraints weight = 4359.423| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.76 r_work: 0.3210 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3870 Z= 0.107 Angle : 0.534 6.530 5268 Z= 0.266 Chirality : 0.040 0.225 614 Planarity : 0.004 0.039 659 Dihedral : 4.507 50.436 535 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.72 % Allowed : 14.32 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.40), residues: 480 helix: 0.15 (0.31), residues: 316 sheet: None (None), residues: 0 loop : -1.32 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.017 0.001 TYR A 264 PHE 0.009 0.001 PHE A 351 TRP 0.011 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 3870) covalent geometry : angle 0.53450 / 0.27 ( 5268) hydrogen bonds : bond 0.03849 / 2.49 ( 184) hydrogen bonds : angle 3.69069 / 2.51 ( 546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.150 Fit side-chains REVERT: A 69 ARG cc_start: 0.8251 (ptp90) cc_final: 0.7960 (ttm110) REVERT: A 112 ASP cc_start: 0.8678 (t0) cc_final: 0.8351 (t0) REVERT: A 286 ARG cc_start: 0.9174 (tpp80) cc_final: 0.8952 (tpp80) REVERT: A 310 ARG cc_start: 0.8314 (mtt180) cc_final: 0.8071 (mtt-85) REVERT: A 349 THR cc_start: 0.7662 (m) cc_final: 0.7408 (m) REVERT: A 369 LEU cc_start: 0.8426 (tp) cc_final: 0.8204 (tp) REVERT: A 417 GLN cc_start: 0.8140 (mt0) cc_final: 0.7773 (mp10) REVERT: A 444 TYR cc_start: 0.8098 (t80) cc_final: 0.7308 (t80) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 0.0851 time to fit residues: 8.0779 Evaluate side-chains 77 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102733 restraints weight = 4368.520| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.77 r_work: 0.3208 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3870 Z= 0.106 Angle : 0.526 5.959 5268 Z= 0.260 Chirality : 0.040 0.228 614 Planarity : 0.004 0.036 659 Dihedral : 4.342 46.440 535 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.46 % Allowed : 15.56 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.40), residues: 480 helix: 0.24 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.26 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.017 0.001 TYR A 264 PHE 0.009 0.001 PHE A 351 TRP 0.011 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 3870) covalent geometry : angle 0.52606 / 0.26 ( 5268) hydrogen bonds : bond 0.03811 / 2.47 ( 184) hydrogen bonds : angle 3.62457 / 2.46 ( 546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.087 Fit side-chains REVERT: A 8 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8638 (mm-40) REVERT: A 69 ARG cc_start: 0.8233 (ptp90) cc_final: 0.7927 (ttm110) REVERT: A 107 ASP cc_start: 0.8068 (m-30) cc_final: 0.7731 (m-30) REVERT: A 112 ASP cc_start: 0.8667 (t0) cc_final: 0.8326 (t0) REVERT: A 286 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8948 (tpp80) REVERT: A 310 ARG cc_start: 0.8329 (mtt180) cc_final: 0.8101 (mtt-85) REVERT: A 336 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7087 (ptp90) REVERT: A 349 THR cc_start: 0.7669 (m) cc_final: 0.7415 (m) REVERT: A 369 LEU cc_start: 0.8346 (tp) cc_final: 0.8126 (tp) REVERT: A 417 GLN cc_start: 0.8146 (mt0) cc_final: 0.7777 (mp10) REVERT: A 444 TYR cc_start: 0.8083 (t80) cc_final: 0.7323 (t80) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.0775 time to fit residues: 7.9314 Evaluate side-chains 80 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095384 restraints weight = 4527.076| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.76 r_work: 0.3070 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3870 Z= 0.266 Angle : 0.702 6.073 5268 Z= 0.351 Chirality : 0.048 0.247 614 Planarity : 0.005 0.051 659 Dihedral : 5.008 55.812 535 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.95 % Allowed : 15.80 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.40), residues: 480 helix: 0.06 (0.30), residues: 315 sheet: -2.78 (1.62), residues: 10 loop : -1.07 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 162 TYR 0.018 0.002 TYR A 354 PHE 0.025 0.002 PHE A 351 TRP 0.015 0.002 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 ( 3870) covalent geometry : angle 0.70158 / 0.35 ( 5268) hydrogen bonds : bond 0.06816 / 4.45 ( 184) hydrogen bonds : angle 4.17396 / 2.86 ( 546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.154 Fit side-chains REVERT: A 112 ASP cc_start: 0.8756 (t0) cc_final: 0.8504 (t0) REVERT: A 310 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7892 (mtt-85) REVERT: A 369 LEU cc_start: 0.8364 (tp) cc_final: 0.8062 (tp) REVERT: A 444 TYR cc_start: 0.8254 (t80) cc_final: 0.7493 (t80) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.0783 time to fit residues: 7.4170 Evaluate side-chains 81 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099262 restraints weight = 4500.209| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.77 r_work: 0.3166 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3870 Z= 0.125 Angle : 0.565 5.658 5268 Z= 0.281 Chirality : 0.041 0.244 614 Planarity : 0.004 0.037 659 Dihedral : 4.637 50.004 535 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.95 % Allowed : 17.04 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.41), residues: 480 helix: 0.36 (0.31), residues: 321 sheet: -2.68 (1.59), residues: 10 loop : -0.68 (0.58), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.017 0.001 TYR A 264 PHE 0.010 0.001 PHE A 351 TRP 0.014 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 3870) covalent geometry : angle 0.56465 / 0.28 ( 5268) hydrogen bonds : bond 0.04405 / 2.86 ( 184) hydrogen bonds : angle 3.79697 / 2.59 ( 546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.087 Fit side-chains REVERT: A 69 ARG cc_start: 0.8157 (ptp90) cc_final: 0.7746 (ttp80) REVERT: A 107 ASP cc_start: 0.8149 (m-30) cc_final: 0.7805 (m-30) REVERT: A 112 ASP cc_start: 0.8721 (t0) cc_final: 0.8413 (t0) REVERT: A 286 ARG cc_start: 0.9094 (tpp80) cc_final: 0.8720 (ptm160) REVERT: A 310 ARG cc_start: 0.8311 (mtt180) cc_final: 0.8097 (mtt-85) REVERT: A 336 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7034 (ptp90) REVERT: A 369 LEU cc_start: 0.8257 (tp) cc_final: 0.8029 (tp) REVERT: A 417 GLN cc_start: 0.8056 (mt0) cc_final: 0.7660 (mp10) REVERT: A 444 TYR cc_start: 0.8172 (t80) cc_final: 0.7383 (t80) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.0501 time to fit residues: 5.1226 Evaluate side-chains 85 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.0010 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099687 restraints weight = 4428.418| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.75 r_work: 0.3167 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3870 Z= 0.129 Angle : 0.572 5.609 5268 Z= 0.284 Chirality : 0.042 0.243 614 Planarity : 0.004 0.038 659 Dihedral : 4.506 48.091 535 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.21 % Allowed : 18.52 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.41), residues: 480 helix: 0.35 (0.30), residues: 328 sheet: -2.54 (1.61), residues: 10 loop : -0.92 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.017 0.001 TYR A 264 PHE 0.012 0.001 PHE A 351 TRP 0.013 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 3870) covalent geometry : angle 0.57207 / 0.28 ( 5268) hydrogen bonds : bond 0.04469 / 2.90 ( 184) hydrogen bonds : angle 3.74224 / 2.54 ( 546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.137 Fit side-chains REVERT: A 69 ARG cc_start: 0.8122 (ptp90) cc_final: 0.7748 (ttp80) REVERT: A 107 ASP cc_start: 0.8176 (m-30) cc_final: 0.7841 (m-30) REVERT: A 112 ASP cc_start: 0.8732 (t0) cc_final: 0.8415 (t0) REVERT: A 293 ARG cc_start: 0.8470 (tmm160) cc_final: 0.7617 (ttm110) REVERT: A 310 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8060 (mtt-85) REVERT: A 336 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6946 (ptp90) REVERT: A 369 LEU cc_start: 0.8236 (tp) cc_final: 0.8009 (tp) REVERT: A 417 GLN cc_start: 0.8056 (mt0) cc_final: 0.7659 (mp10) REVERT: A 444 TYR cc_start: 0.8176 (t80) cc_final: 0.7399 (t80) outliers start: 13 outliers final: 11 residues processed: 82 average time/residue: 0.0762 time to fit residues: 7.6658 Evaluate side-chains 83 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100550 restraints weight = 4367.513| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.71 r_work: 0.3218 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3870 Z= 0.124 Angle : 0.574 6.048 5268 Z= 0.283 Chirality : 0.041 0.243 614 Planarity : 0.004 0.036 659 Dihedral : 4.422 45.731 535 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.46 % Allowed : 18.77 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.41), residues: 480 helix: 0.40 (0.30), residues: 329 sheet: -2.59 (1.61), residues: 10 loop : -0.86 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 162 TYR 0.017 0.001 TYR A 264 PHE 0.011 0.001 PHE A 351 TRP 0.013 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 3870) covalent geometry : angle 0.57418 / 0.28 ( 5268) hydrogen bonds : bond 0.04214 / 2.74 ( 184) hydrogen bonds : angle 3.68904 / 2.50 ( 546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.142 Fit side-chains REVERT: A 69 ARG cc_start: 0.8108 (ptp90) cc_final: 0.7751 (ttp80) REVERT: A 107 ASP cc_start: 0.8161 (m-30) cc_final: 0.7822 (m-30) REVERT: A 112 ASP cc_start: 0.8739 (t0) cc_final: 0.8406 (t0) REVERT: A 293 ARG cc_start: 0.8472 (tmm160) cc_final: 0.7622 (ttm110) REVERT: A 336 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6886 (ptp90) REVERT: A 369 LEU cc_start: 0.8223 (tp) cc_final: 0.8001 (tp) REVERT: A 417 GLN cc_start: 0.8061 (mt0) cc_final: 0.7645 (mp10) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.0638 time to fit residues: 6.3292 Evaluate side-chains 84 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 0.0070 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 0.0030 chunk 39 optimal weight: 2.9990 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105007 restraints weight = 4562.505| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.66 r_work: 0.3256 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3870 Z= 0.108 Angle : 0.556 6.289 5268 Z= 0.273 Chirality : 0.040 0.240 614 Planarity : 0.004 0.036 659 Dihedral : 4.204 40.077 535 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.96 % Allowed : 18.77 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.41), residues: 480 helix: 0.54 (0.31), residues: 328 sheet: -2.70 (1.57), residues: 10 loop : -0.69 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 134 TYR 0.017 0.001 TYR A 264 PHE 0.007 0.001 PHE A 438 TRP 0.011 0.001 TRP A 346 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 3870) covalent geometry : angle 0.55605 / 0.27 ( 5268) hydrogen bonds : bond 0.03403 / 2.21 ( 184) hydrogen bonds : angle 3.58707 / 2.42 ( 546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8143 (ptp90) cc_final: 0.7779 (ttm110) REVERT: A 107 ASP cc_start: 0.8124 (m-30) cc_final: 0.7832 (m-30) REVERT: A 112 ASP cc_start: 0.8652 (t0) cc_final: 0.8354 (t0) REVERT: A 293 ARG cc_start: 0.8489 (tmm160) cc_final: 0.7692 (ttm110) REVERT: A 336 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6959 (ptp90) REVERT: A 349 THR cc_start: 0.7731 (m) cc_final: 0.7472 (m) REVERT: A 369 LEU cc_start: 0.8384 (tp) cc_final: 0.8170 (tp) REVERT: A 417 GLN cc_start: 0.8104 (mt0) cc_final: 0.7710 (mp10) REVERT: A 458 MET cc_start: 0.7969 (tpp) cc_final: 0.7766 (tpp) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.0477 time to fit residues: 4.6523 Evaluate side-chains 82 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.0050 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 17 optimal weight: 0.0670 chunk 27 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.1132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.159984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113648 restraints weight = 4464.589| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.74 r_work: 0.3295 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3870 Z= 0.100 Angle : 0.537 6.383 5268 Z= 0.261 Chirality : 0.039 0.232 614 Planarity : 0.004 0.036 659 Dihedral : 3.880 31.853 535 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.98 % Allowed : 19.75 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.42), residues: 480 helix: 0.74 (0.31), residues: 327 sheet: -2.89 (1.49), residues: 10 loop : -0.52 (0.59), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.018 0.001 TYR A 264 PHE 0.007 0.001 PHE A 347 TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 3870) covalent geometry : angle 0.53723 / 0.26 ( 5268) hydrogen bonds : bond 0.02545 / 1.66 ( 184) hydrogen bonds : angle 3.47982 / 2.35 ( 546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1013.92 seconds wall clock time: 18 minutes 1.22 seconds (1081.22 seconds total)