Starting phenix.real_space_refine on Tue Aug 4 12:52:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kkn_62393/08_2026/9kkn_62393.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kkn_62393/08_2026/9kkn_62393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kkn_62393/08_2026/9kkn_62393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kkn_62393/08_2026/9kkn_62393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kkn_62393/08_2026/9kkn_62393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kkn_62393/08_2026/9kkn_62393.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.083 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 17 5.16 5 C 2013 2.51 5 N 487 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 3039 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3029 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.94, per 1000 atoms: 0.31 Number of scatterers: 3039 At special positions: 0 Unit cell: (72.696, 58.716, 65.24, 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 17 16.00 O 522 8.00 N 487 7.00 C 2013 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: 0.29 Conformation dependent library (CDL) restraints added in 123.7 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 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: 23 helices and 0 sheets defined 91.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 26 through 57 removed outlier: 4.747A pdb=" N VAL A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 58 through 61 removed outlier: 3.843A pdb=" N ILE A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 122 through 149 removed outlier: 4.622A pdb=" N LYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 140 - end of helix Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 151 through 171 Processing helix chain 'A' and resid 174 through 204 removed outlier: 3.656A pdb=" N LEU A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.673A pdb=" N ARG A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.278A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.553A pdb=" N ASP A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 Proline residue: A 304 - end of helix removed outlier: 3.631A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.716A pdb=" N ARG A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 374 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 379 through 413 removed outlier: 3.656A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'A' and resid 417 through 446 removed outlier: 3.875A pdb=" N ILE A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 6.017A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 475 245 hydrogen bonds defined for protein. 729 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: 0.50 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 468 1.32 - 1.44: 802 1.44 - 1.56: 1815 1.56 - 1.68: 0 1.68 - 1.80: 28 Bond restraints: 3113 Sorted by residual: bond pdb=" CA SER A 323 " pdb=" C SER A 323 " ideal model delta sigma weight residual 1.528 1.506 0.023 1.39e-02 5.18e+03 2.67e+00 bond pdb=" C VAL A 438 " pdb=" O VAL A 438 " ideal model delta sigma weight residual 1.241 1.226 0.015 1.06e-02 8.90e+03 1.96e+00 bond pdb=" C3 ACH A 601 " pdb=" O4 ACH A 601 " ideal model delta sigma weight residual 1.424 1.452 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C VAL A 54 " pdb=" O VAL A 54 " ideal model delta sigma weight residual 1.240 1.223 0.016 1.26e-02 6.30e+03 1.67e+00 bond pdb=" C SER A 222 " pdb=" O SER A 222 " ideal model delta sigma weight residual 1.237 1.222 0.015 1.17e-02 7.31e+03 1.66e+00 ... (remaining 3108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 4147 1.83 - 3.66: 83 3.66 - 5.49: 22 5.49 - 7.32: 8 7.32 - 9.15: 1 Bond angle restraints: 4261 Sorted by residual: angle pdb=" C VAL A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta sigma weight residual 119.87 115.13 4.74 1.04e+00 9.25e-01 2.08e+01 angle pdb=" N VAL A 122 " pdb=" CA VAL A 122 " pdb=" C VAL A 122 " ideal model delta sigma weight residual 112.96 108.69 4.27 1.00e+00 1.00e+00 1.82e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 111.09 115.79 -4.70 1.25e+00 6.40e-01 1.41e+01 angle pdb=" C VAL A 438 " pdb=" CA VAL A 438 " pdb=" CB VAL A 438 " ideal model delta sigma weight residual 110.88 107.31 3.57 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C VAL A 52 " pdb=" CA VAL A 52 " pdb=" CB VAL A 52 " ideal model delta sigma weight residual 112.26 107.40 4.86 1.62e+00 3.81e-01 9.00e+00 ... (remaining 4256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.10: 1604 12.10 - 24.20: 162 24.20 - 36.30: 48 36.30 - 48.39: 12 48.39 - 60.49: 11 Dihedral angle restraints: 1837 sinusoidal: 667 harmonic: 1170 Sorted by residual: dihedral pdb=" CA TYR A 421 " pdb=" C TYR A 421 " pdb=" N ALA A 422 " pdb=" CA ALA A 422 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta harmonic sigma weight residual -180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" N GLN A 185 " pdb=" CA GLN A 185 " pdb=" CB GLN A 185 " pdb=" CG GLN A 185 " ideal model delta sinusoidal sigma weight residual -180.00 -120.77 -59.23 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 277 0.027 - 0.054: 139 0.054 - 0.081: 58 0.081 - 0.108: 34 0.108 - 0.135: 10 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA VAL A 374 " pdb=" N VAL A 374 " pdb=" C VAL A 374 " pdb=" CB VAL A 374 " both_signs ideal model delta sigma weight residual False 2.44 2.31 0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PRO A 353 " pdb=" N PRO A 353 " pdb=" C PRO A 353 " pdb=" CB PRO A 353 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA PRO A 205 " pdb=" N PRO A 205 " pdb=" C PRO A 205 " pdb=" CB PRO A 205 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 515 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 336 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 337 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 228 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 229 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 229 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 230 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " -0.020 5.00e-02 4.00e+02 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 923 2.82 - 3.34: 3141 3.34 - 3.86: 5314 3.86 - 4.38: 6024 4.38 - 4.90: 10301 Nonbonded interactions: 25703 Sorted by model distance: nonbonded pdb=" O ALA A 172 " pdb=" NZ LYS A 241 " model vdw 2.301 3.120 nonbonded pdb=" NE2 GLN A 135 " pdb=" OG SER A 189 " model vdw 2.302 3.120 nonbonded pdb=" O LEU A 43 " pdb=" ND2 ASN A 47 " model vdw 2.322 3.120 nonbonded pdb=" N ASP A 152 " pdb=" OD1 ASP A 152 " model vdw 2.439 3.120 nonbonded pdb=" O ALA A 395 " pdb=" OG1 THR A 399 " model vdw 2.469 3.040 ... (remaining 25698 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.970 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.005 0.038 3113 Z= 0.226 Angle : 0.738 9.147 4261 Z= 0.394 Chirality : 0.043 0.135 518 Planarity : 0.005 0.042 529 Dihedral : 12.683 60.493 1085 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.32 % Allowed : 13.61 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.75 (0.38), residues: 400 helix: -0.55 (0.26), residues: 332 sheet: None (None), residues: 0 loop : -3.61 (0.60), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.009 0.001 TYR A 421 PHE 0.010 0.001 PHE A 407 TRP 0.009 0.001 TRP A 331 HIS 0.001 0.000 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 ( 3113) covalent geometry : angle 0.73758 / 0.39 ( 4261) hydrogen bonds : bond 0.12679 / 8.62 ( 245) hydrogen bonds : angle 6.62552 / 4.50 ( 729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.065 Fit side-chains REVERT: A 51 MET cc_start: 0.8658 (mmt) cc_final: 0.8431 (mmp) REVERT: A 317 LYS cc_start: 0.8328 (tttp) cc_final: 0.8113 (tptt) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.4278 time to fit residues: 23.7143 Evaluate side-chains 38 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.0370 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105926 restraints weight = 3789.150| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.95 r_work: 0.3224 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3113 Z= 0.140 Angle : 0.668 7.851 4261 Z= 0.314 Chirality : 0.041 0.133 518 Planarity : 0.005 0.037 529 Dihedral : 4.639 29.099 439 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.16 % Allowed : 17.09 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.43), residues: 400 helix: 0.96 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -2.57 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 378 TYR 0.008 0.001 TYR A 421 PHE 0.008 0.001 PHE A 335 TRP 0.006 0.001 TRP A 325 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 3113) covalent geometry : angle 0.66828 / 0.31 ( 4261) hydrogen bonds : bond 0.04014 / 2.63 ( 245) hydrogen bonds : angle 4.66961 / 3.15 ( 729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.105 Fit side-chains REVERT: A 209 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7036 (mt-10) outliers start: 10 outliers final: 1 residues processed: 46 average time/residue: 0.3621 time to fit residues: 17.2246 Evaluate side-chains 39 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107114 restraints weight = 3729.106| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.95 r_work: 0.3228 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3113 Z= 0.136 Angle : 0.652 8.032 4261 Z= 0.303 Chirality : 0.042 0.246 518 Planarity : 0.005 0.040 529 Dihedral : 4.176 18.033 438 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.90 % Allowed : 18.35 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.44), residues: 400 helix: 1.47 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.92 (0.75), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.014 0.001 TYR A 50 PHE 0.008 0.001 PHE A 407 TRP 0.006 0.001 TRP A 331 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 3113) covalent geometry : angle 0.65179 / 0.30 ( 4261) hydrogen bonds : bond 0.03784 / 2.48 ( 245) hydrogen bonds : angle 4.38479 / 2.95 ( 729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.103 Fit side-chains REVERT: A 206 GLU cc_start: 0.6657 (pp20) cc_final: 0.6091 (pp20) REVERT: A 209 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6977 (mt-10) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.4046 time to fit residues: 22.1257 Evaluate side-chains 47 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.0030 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109397 restraints weight = 3687.584| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.88 r_work: 0.3282 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3113 Z= 0.126 Angle : 0.641 7.585 4261 Z= 0.296 Chirality : 0.041 0.196 518 Planarity : 0.005 0.041 529 Dihedral : 4.052 18.339 438 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.11 % Allowed : 19.30 % Favored : 76.58 % 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: 1.86 (0.44), residues: 400 helix: 1.76 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.54 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.011 0.001 TYR A 50 PHE 0.008 0.001 PHE A 407 TRP 0.005 0.001 TRP A 315 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 3113) covalent geometry : angle 0.64126 / 0.30 ( 4261) hydrogen bonds : bond 0.03485 / 2.28 ( 245) hydrogen bonds : angle 4.23707 / 2.85 ( 729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.108 Fit side-chains REVERT: A 173 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: A 174 ASP cc_start: 0.7979 (t0) cc_final: 0.7768 (t0) REVERT: A 177 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7582 (t) REVERT: A 206 GLU cc_start: 0.6628 (pp20) cc_final: 0.6064 (pp20) REVERT: A 209 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 301 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8593 (p) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 0.3894 time to fit residues: 23.2992 Evaluate side-chains 56 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107048 restraints weight = 3686.473| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.93 r_work: 0.3248 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3113 Z= 0.140 Angle : 0.645 8.065 4261 Z= 0.299 Chirality : 0.042 0.233 518 Planarity : 0.005 0.040 529 Dihedral : 4.020 20.094 438 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.48 % Allowed : 21.20 % Favored : 75.32 % 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: 1.93 (0.44), residues: 400 helix: 1.80 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.44 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.010 0.001 TYR A 50 PHE 0.007 0.001 PHE A 407 TRP 0.006 0.001 TRP A 331 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 3113) covalent geometry : angle 0.64541 / 0.30 ( 4261) hydrogen bonds : bond 0.03663 / 2.39 ( 245) hydrogen bonds : angle 4.22082 / 2.84 ( 729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.063 Fit side-chains REVERT: A 301 CYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 450 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6816 (mp10) outliers start: 11 outliers final: 9 residues processed: 52 average time/residue: 0.2583 time to fit residues: 13.9984 Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 2 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.2094 > 50:) chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106429 restraints weight = 3713.802| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.93 r_work: 0.3230 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3113 Z= 0.147 Angle : 0.649 7.694 4261 Z= 0.303 Chirality : 0.042 0.222 518 Planarity : 0.005 0.041 529 Dihedral : 4.053 20.028 438 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.38 % Allowed : 19.30 % Favored : 75.32 % 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: 1.97 (0.44), residues: 400 helix: 1.82 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.44 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.017 0.001 TYR A 50 PHE 0.007 0.001 PHE A 407 TRP 0.006 0.001 TRP A 331 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 3113) covalent geometry : angle 0.64907 / 0.30 ( 4261) hydrogen bonds : bond 0.03746 / 2.44 ( 245) hydrogen bonds : angle 4.24954 / 2.86 ( 729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.106 Fit side-chains REVERT: A 177 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7620 (t) REVERT: A 301 CYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8568 (p) REVERT: A 329 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7628 (mmm) REVERT: A 450 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6817 (mp10) outliers start: 17 outliers final: 12 residues processed: 53 average time/residue: 0.2671 time to fit residues: 14.8442 Evaluate side-chains 54 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107009 restraints weight = 3744.742| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.93 r_work: 0.3244 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3113 Z= 0.138 Angle : 0.649 9.139 4261 Z= 0.301 Chirality : 0.043 0.290 518 Planarity : 0.005 0.041 529 Dihedral : 4.018 18.716 438 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.75 % Allowed : 20.57 % Favored : 74.68 % 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: 2.08 (0.44), residues: 400 helix: 1.90 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.40 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.017 0.001 TYR A 50 PHE 0.007 0.001 PHE A 407 TRP 0.006 0.001 TRP A 331 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 3113) covalent geometry : angle 0.64923 / 0.30 ( 4261) hydrogen bonds : bond 0.03657 / 2.39 ( 245) hydrogen bonds : angle 4.21393 / 2.83 ( 729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.066 Fit side-chains REVERT: A 177 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7634 (t) REVERT: A 206 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5940 (pp20) REVERT: A 301 CYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 450 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6827 (mp10) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 0.2880 time to fit residues: 14.9824 Evaluate side-chains 54 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106725 restraints weight = 3808.852| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.97 r_work: 0.3241 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3113 Z= 0.143 Angle : 0.655 8.741 4261 Z= 0.304 Chirality : 0.043 0.271 518 Planarity : 0.005 0.041 529 Dihedral : 4.027 18.444 438 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.75 % Allowed : 21.84 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.44), residues: 400 helix: 1.91 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.41 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.015 0.001 TYR A 50 PHE 0.007 0.001 PHE A 407 TRP 0.006 0.001 TRP A 331 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 ( 3113) covalent geometry : angle 0.65467 / 0.30 ( 4261) hydrogen bonds : bond 0.03711 / 2.43 ( 245) hydrogen bonds : angle 4.23324 / 2.84 ( 729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.093 Fit side-chains REVERT: A 167 VAL cc_start: 0.7970 (t) cc_final: 0.7744 (t) REVERT: A 177 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7631 (t) REVERT: A 206 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5984 (pp20) REVERT: A 301 CYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8585 (p) REVERT: A 450 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.6851 (mp10) outliers start: 15 outliers final: 11 residues processed: 49 average time/residue: 0.2699 time to fit residues: 13.7464 Evaluate side-chains 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 3 optimal weight: 0.0060 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108983 restraints weight = 3812.292| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.91 r_work: 0.3254 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3113 Z= 0.126 Angle : 0.638 8.316 4261 Z= 0.296 Chirality : 0.042 0.257 518 Planarity : 0.005 0.041 529 Dihedral : 3.967 17.069 438 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.75 % Allowed : 21.84 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.44), residues: 400 helix: 2.03 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.37 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.014 0.001 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.005 0.001 TRP A 331 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3113) covalent geometry : angle 0.63814 / 0.30 ( 4261) hydrogen bonds : bond 0.03462 / 2.28 ( 245) hydrogen bonds : angle 4.17116 / 2.79 ( 729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.068 Fit side-chains REVERT: A 167 VAL cc_start: 0.7952 (t) cc_final: 0.7731 (t) REVERT: A 177 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7619 (t) REVERT: A 206 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6001 (pp20) REVERT: A 450 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6899 (mp10) outliers start: 15 outliers final: 8 residues processed: 51 average time/residue: 0.3560 time to fit residues: 18.7928 Evaluate side-chains 50 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.0170 chunk 38 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108316 restraints weight = 3712.714| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.95 r_work: 0.3259 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3113 Z= 0.130 Angle : 0.650 7.871 4261 Z= 0.301 Chirality : 0.042 0.237 518 Planarity : 0.005 0.041 529 Dihedral : 3.958 16.668 438 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.80 % Allowed : 23.10 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.44), residues: 400 helix: 2.00 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.26 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.026 0.001 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.006 0.001 TRP A 331 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 3113) covalent geometry : angle 0.64963 / 0.30 ( 4261) hydrogen bonds : bond 0.03496 / 2.30 ( 245) hydrogen bonds : angle 4.20649 / 2.82 ( 729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.063 Fit side-chains REVERT: A 167 VAL cc_start: 0.7948 (t) cc_final: 0.7735 (t) REVERT: A 177 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7614 (t) REVERT: A 206 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6074 (pp20) REVERT: A 301 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8546 (p) REVERT: A 450 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6881 (mp10) outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 0.2577 time to fit residues: 12.9197 Evaluate side-chains 50 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.0050 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108554 restraints weight = 3734.373| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.95 r_work: 0.3257 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3113 Z= 0.130 Angle : 0.652 7.824 4261 Z= 0.302 Chirality : 0.042 0.234 518 Planarity : 0.005 0.041 529 Dihedral : 3.939 16.514 438 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.80 % Allowed : 23.42 % Favored : 72.78 % 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: 2.27 (0.44), residues: 400 helix: 2.01 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.21 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.025 0.001 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.006 0.001 TRP A 331 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 3113) covalent geometry : angle 0.65197 / 0.30 ( 4261) hydrogen bonds : bond 0.03465 / 2.28 ( 245) hydrogen bonds : angle 4.19898 / 2.82 ( 729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 909.82 seconds wall clock time: 16 minutes 11.07 seconds (971.07 seconds total)