Starting phenix.real_space_refine on Tue Aug 4 13:22:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l38_62783/08_2026/9l38_62783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l38_62783/08_2026/9l38_62783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l38_62783/08_2026/9l38_62783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l38_62783/08_2026/9l38_62783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l38_62783/08_2026/9l38_62783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l38_62783/08_2026/9l38_62783.map" } resolution = 3.2 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= -0.001 sd= 0.024 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 20 5.16 5 C 2194 2.51 5 N 513 2.21 5 O 541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 3268 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3267 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 0.89, per 1000 atoms: 0.27 Number of scatterers: 3268 At special positions: 0 Unit cell: (74.226, 50.874, 68.388, 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 20 16.00 O 541 8.00 N 513 7.00 C 2194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 480 " distance=2.03 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: 0.18 Conformation dependent library (CDL) restraints added in 87.6 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 87.4% 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 5 through 23 Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.867A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 84 through 118 removed outlier: 7.609A pdb=" N THR A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N THR A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 125 through 146 Proline residue: A 131 - end of helix removed outlier: 4.032A pdb=" N GLN A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 169 through 183 removed outlier: 4.201A pdb=" N PHE A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 207 removed outlier: 3.594A pdb=" N SER A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.644A pdb=" N TYR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 307 removed outlier: 5.077A pdb=" N ASN A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 327 through 350 Proline residue: A 333 - end of helix removed outlier: 3.714A pdb=" N GLY A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 385 removed outlier: 3.593A pdb=" N VAL A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 389 through 416 removed outlier: 4.132A pdb=" N LEU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.557A pdb=" N SER A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.544A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 248 hydrogen bonds defined for protein. 738 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: 0.51 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 951 1.35 - 1.46: 931 1.46 - 1.58: 1450 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 3362 Sorted by residual: bond pdb=" C TRP A 30 " pdb=" N PRO A 31 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.54e+00 bond pdb=" CB THR A 357 " pdb=" OG1 THR A 357 " ideal model delta sigma weight residual 1.433 1.417 0.016 1.60e-02 3.91e+03 1.00e+00 bond pdb=" CB VAL A 34 " pdb=" CG2 VAL A 34 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.64e-01 bond pdb=" CA PHE A 86 " pdb=" C PHE A 86 " ideal model delta sigma weight residual 1.521 1.528 -0.008 1.14e-02 7.69e+03 4.48e-01 bond pdb=" C PHE A 86 " pdb=" O PHE A 86 " ideal model delta sigma weight residual 1.244 1.238 0.006 1.00e-02 1.00e+04 3.09e-01 ... (remaining 3357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 4426 1.06 - 2.12: 114 2.12 - 3.18: 20 3.18 - 4.24: 3 4.24 - 5.29: 9 Bond angle restraints: 4572 Sorted by residual: angle pdb=" N GLY A 29 " pdb=" CA GLY A 29 " pdb=" C GLY A 29 " ideal model delta sigma weight residual 115.72 112.58 3.14 1.51e+00 4.39e-01 4.32e+00 angle pdb=" CA TRP A 285 " pdb=" CB TRP A 285 " pdb=" CG TRP A 285 " ideal model delta sigma weight residual 113.60 116.66 -3.06 1.90e+00 2.77e-01 2.59e+00 angle pdb=" C HIS A 212 " pdb=" N ILE A 213 " pdb=" CA ILE A 213 " ideal model delta sigma weight residual 122.60 121.56 1.04 6.80e-01 2.16e+00 2.34e+00 angle pdb=" N TRP A 30 " pdb=" CA TRP A 30 " pdb=" CB TRP A 30 " ideal model delta sigma weight residual 110.43 108.12 2.31 1.55e+00 4.16e-01 2.22e+00 angle pdb=" C GLY A 29 " pdb=" N TRP A 30 " pdb=" CA TRP A 30 " ideal model delta sigma weight residual 120.09 121.93 -1.84 1.25e+00 6.40e-01 2.17e+00 ... (remaining 4567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 1758 11.89 - 23.78: 120 23.78 - 35.67: 36 35.67 - 47.56: 6 47.56 - 59.45: 5 Dihedral angle restraints: 1925 sinusoidal: 726 harmonic: 1199 Sorted by residual: dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N GLY A 29 " pdb=" CA GLY A 29 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" N LEU A 17 " pdb=" CA LEU A 17 " pdb=" CB LEU A 17 " pdb=" CG LEU A 17 " ideal model delta sinusoidal sigma weight residual -180.00 -120.55 -59.45 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 388 " pdb=" CA LEU A 388 " pdb=" CB LEU A 388 " pdb=" CG LEU A 388 " ideal model delta sinusoidal sigma weight residual -180.00 -125.32 -54.68 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 1922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 318 0.024 - 0.048: 124 0.048 - 0.072: 58 0.072 - 0.097: 25 0.097 - 0.121: 8 Chirality restraints: 533 Sorted by residual: chirality pdb=" CA MET A 130 " pdb=" N MET A 130 " pdb=" C MET A 130 " pdb=" CB MET A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA PHE A 441 " pdb=" N PHE A 441 " pdb=" C PHE A 441 " pdb=" CB PHE A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.99e-01 ... (remaining 530 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 30 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 31 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 385 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO A 386 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 386 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 386 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 130 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.54e-01 pdb=" N PRO A 131 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.013 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 606 2.76 - 3.30: 3436 3.30 - 3.83: 5959 3.83 - 4.37: 6807 4.37 - 4.90: 11342 Nonbonded interactions: 28150 Sorted by model distance: nonbonded pdb=" O ILE A 466 " pdb=" OG1 THR A 469 " model vdw 2.226 3.040 nonbonded pdb=" O ALA A 410 " pdb=" OG1 THR A 414 " model vdw 2.240 3.040 nonbonded pdb=" O PRO A 131 " pdb=" OG1 THR A 134 " model vdw 2.243 3.040 nonbonded pdb=" O ILE A 114 " pdb=" OG1 THR A 118 " model vdw 2.264 3.040 nonbonded pdb=" O ILE A 159 " pdb=" ND2 ASN A 163 " model vdw 2.341 3.120 ... (remaining 28145 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.360 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.002 0.022 3363 Z= 0.107 Angle : 0.465 5.295 4574 Z= 0.253 Chirality : 0.036 0.121 533 Planarity : 0.004 0.027 552 Dihedral : 9.764 59.452 1146 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.54 % Allowed : 3.11 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.10 (0.43), residues: 402 helix: 1.57 (0.29), residues: 335 sheet: None (None), residues: 0 loop : 0.86 (0.86), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.003 0.001 TYR A 318 PHE 0.012 0.001 PHE A 379 TRP 0.014 0.002 TRP A 285 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 3362) covalent geometry : angle 0.46474 / 0.25 ( 4572) SS BOND : bond 0.00056 / 0.04 ( 1) SS BOND : angle 0.71151 / 0.27 ( 2) hydrogen bonds : bond 0.17507 / 12.05 ( 248) hydrogen bonds : angle 6.70351 / 4.99 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.122 Fit side-chains REVERT: A 210 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6896 (ttm-80) REVERT: A 327 PHE cc_start: 0.7703 (p90) cc_final: 0.7427 (p90) REVERT: A 398 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8610 (tm-30) outliers start: 9 outliers final: 1 residues processed: 112 average time/residue: 0.0750 time to fit residues: 10.0880 Evaluate side-chains 81 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138578 restraints weight = 4101.026| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.97 r_work: 0.3459 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3363 Z= 0.157 Angle : 0.571 5.084 4574 Z= 0.292 Chirality : 0.041 0.227 533 Planarity : 0.005 0.038 552 Dihedral : 5.274 45.761 441 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.39 % Allowed : 11.86 % Favored : 84.75 % 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: 2.68 (0.43), residues: 402 helix: 1.97 (0.29), residues: 341 sheet: None (None), residues: 0 loop : 0.91 (0.91), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.013 0.001 TYR A 223 PHE 0.017 0.002 PHE A 474 TRP 0.014 0.002 TRP A 285 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 3362) covalent geometry : angle 0.57085 / 0.29 ( 4572) SS BOND : bond 0.00168 / 0.10 ( 1) SS BOND : angle 0.50590 / 0.21 ( 2) hydrogen bonds : bond 0.04214 / 2.98 ( 248) hydrogen bonds : angle 4.34022 / 3.26 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.116 Fit side-chains REVERT: A 182 LYS cc_start: 0.8398 (mttt) cc_final: 0.7598 (mmmt) REVERT: A 301 ASN cc_start: 0.8212 (t0) cc_final: 0.7722 (m-40) REVERT: A 346 TYR cc_start: 0.7426 (m-80) cc_final: 0.7222 (m-80) REVERT: A 400 ILE cc_start: 0.8572 (mt) cc_final: 0.8358 (mt) outliers start: 12 outliers final: 6 residues processed: 92 average time/residue: 0.0554 time to fit residues: 6.3608 Evaluate side-chains 79 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 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 = 0.3753 r_free = 0.3753 target = 0.155409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136070 restraints weight = 4088.177| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.95 r_work: 0.3392 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3363 Z= 0.174 Angle : 0.579 6.060 4574 Z= 0.292 Chirality : 0.041 0.144 533 Planarity : 0.004 0.042 552 Dihedral : 4.478 46.540 438 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.82 % Allowed : 14.97 % Favored : 82.20 % 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: 2.55 (0.43), residues: 402 helix: 1.90 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.74 (0.91), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 101 TYR 0.013 0.001 TYR A 223 PHE 0.020 0.002 PHE A 462 TRP 0.015 0.002 TRP A 285 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 3362) covalent geometry : angle 0.57899 / 0.29 ( 4572) SS BOND : bond 0.00193 / 0.12 ( 1) SS BOND : angle 0.37906 / 0.17 ( 2) hydrogen bonds : bond 0.03981 / 2.85 ( 248) hydrogen bonds : angle 4.21534 / 3.15 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.115 Fit side-chains REVERT: A 80 MET cc_start: 0.8609 (mmt) cc_final: 0.8409 (mmm) REVERT: A 182 LYS cc_start: 0.8395 (mttt) cc_final: 0.7614 (mmmt) REVERT: A 185 SER cc_start: 0.8264 (t) cc_final: 0.8002 (m) REVERT: A 301 ASN cc_start: 0.8214 (t0) cc_final: 0.7786 (m-40) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.0528 time to fit residues: 6.0755 Evaluate side-chains 84 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.0670 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136411 restraints weight = 4092.892| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.95 r_work: 0.3412 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3363 Z= 0.140 Angle : 0.544 5.084 4574 Z= 0.273 Chirality : 0.039 0.142 533 Planarity : 0.004 0.043 552 Dihedral : 4.484 47.513 438 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.39 % Allowed : 16.67 % Favored : 79.94 % 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: 2.56 (0.43), residues: 402 helix: 1.92 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.68 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.012 0.001 TYR A 223 PHE 0.014 0.001 PHE A 462 TRP 0.015 0.002 TRP A 285 HIS 0.002 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3362) covalent geometry : angle 0.54440 / 0.27 ( 4572) SS BOND : bond 0.00056 / 0.04 ( 1) SS BOND : angle 0.31863 / 0.13 ( 2) hydrogen bonds : bond 0.03686 / 2.64 ( 248) hydrogen bonds : angle 4.10699 / 3.09 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.119 Fit side-chains REVERT: A 76 LEU cc_start: 0.8514 (tp) cc_final: 0.8267 (tp) REVERT: A 182 LYS cc_start: 0.8379 (mttt) cc_final: 0.7631 (mmmt) REVERT: A 185 SER cc_start: 0.8323 (t) cc_final: 0.8079 (m) REVERT: A 301 ASN cc_start: 0.8203 (t0) cc_final: 0.7791 (m-40) REVERT: A 343 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8700 (tttt) outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 0.0519 time to fit residues: 6.2517 Evaluate side-chains 85 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.152964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133106 restraints weight = 4094.732| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.96 r_work: 0.3371 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3363 Z= 0.191 Angle : 0.605 6.303 4574 Z= 0.303 Chirality : 0.042 0.210 533 Planarity : 0.004 0.044 552 Dihedral : 4.537 47.754 438 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.11 % Allowed : 18.08 % Favored : 78.81 % 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 (0.43), residues: 402 helix: 1.76 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.30 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.011 0.001 TYR A 223 PHE 0.020 0.002 PHE A 462 TRP 0.016 0.002 TRP A 285 HIS 0.003 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 3362) covalent geometry : angle 0.60544 / 0.30 ( 4572) SS BOND : bond 0.00157 / 0.10 ( 1) SS BOND : angle 0.27655 / 0.12 ( 2) hydrogen bonds : bond 0.03925 / 2.80 ( 248) hydrogen bonds : angle 4.22152 / 3.15 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.115 Fit side-chains REVERT: A 182 LYS cc_start: 0.8359 (mttt) cc_final: 0.7622 (mmmt) REVERT: A 343 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8702 (tttt) REVERT: A 398 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8968 (tm-30) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.0464 time to fit residues: 5.6508 Evaluate side-chains 90 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.155111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135614 restraints weight = 4047.355| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.92 r_work: 0.3402 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3363 Z= 0.147 Angle : 0.573 6.624 4574 Z= 0.287 Chirality : 0.040 0.168 533 Planarity : 0.005 0.075 552 Dihedral : 4.538 48.366 438 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.67 % Allowed : 18.36 % Favored : 77.97 % 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: 2.32 (0.42), residues: 402 helix: 1.79 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.34 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.011 0.001 TYR A 273 PHE 0.014 0.001 PHE A 462 TRP 0.016 0.002 TRP A 285 HIS 0.002 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3362) covalent geometry : angle 0.57328 / 0.29 ( 4572) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 0.29981 / 0.11 ( 2) hydrogen bonds : bond 0.03678 / 2.62 ( 248) hydrogen bonds : angle 4.11537 / 3.10 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.069 Fit side-chains REVERT: A 182 LYS cc_start: 0.8316 (mttt) cc_final: 0.7583 (mmmt) REVERT: A 184 ILE cc_start: 0.7829 (tp) cc_final: 0.7400 (tp) REVERT: A 301 ASN cc_start: 0.8242 (t0) cc_final: 0.7798 (m-40) REVERT: A 343 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8710 (tttt) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.0445 time to fit residues: 5.3977 Evaluate side-chains 88 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.154627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134826 restraints weight = 4102.875| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.98 r_work: 0.3397 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3363 Z= 0.155 Angle : 0.579 6.178 4574 Z= 0.290 Chirality : 0.040 0.149 533 Planarity : 0.005 0.070 552 Dihedral : 4.492 47.328 438 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.39 % Allowed : 18.64 % Favored : 77.97 % 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: 2.30 (0.42), residues: 402 helix: 1.79 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.23 (0.84), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.012 0.001 TYR A 273 PHE 0.016 0.001 PHE A 462 TRP 0.015 0.002 TRP A 285 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 3362) covalent geometry : angle 0.57911 / 0.29 ( 4572) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.26728 / 0.09 ( 2) hydrogen bonds : bond 0.03698 / 2.63 ( 248) hydrogen bonds : angle 4.10458 / 3.09 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.117 Fit side-chains REVERT: A 182 LYS cc_start: 0.8271 (mttt) cc_final: 0.7549 (mmmt) REVERT: A 301 ASN cc_start: 0.8247 (t0) cc_final: 0.7770 (m-40) REVERT: A 343 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8673 (tttt) outliers start: 12 outliers final: 10 residues processed: 87 average time/residue: 0.0516 time to fit residues: 5.7639 Evaluate side-chains 85 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.152652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132828 restraints weight = 4140.345| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.98 r_work: 0.3364 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3363 Z= 0.183 Angle : 0.603 5.869 4574 Z= 0.302 Chirality : 0.041 0.161 533 Planarity : 0.005 0.063 552 Dihedral : 4.559 47.100 438 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.39 % Allowed : 18.36 % Favored : 78.25 % 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: 2.12 (0.42), residues: 402 helix: 1.66 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.23 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.013 0.001 TYR A 273 PHE 0.018 0.002 PHE A 462 TRP 0.015 0.002 TRP A 285 HIS 0.003 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 3362) covalent geometry : angle 0.60350 / 0.30 ( 4572) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.27038 / 0.09 ( 2) hydrogen bonds : bond 0.03829 / 2.72 ( 248) hydrogen bonds : angle 4.16148 / 3.12 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.068 Fit side-chains REVERT: A 182 LYS cc_start: 0.8273 (mttt) cc_final: 0.7560 (mmmt) REVERT: A 301 ASN cc_start: 0.8253 (t0) cc_final: 0.7781 (m-40) REVERT: A 343 LYS cc_start: 0.8983 (ttpt) cc_final: 0.8675 (tttt) outliers start: 12 outliers final: 12 residues processed: 88 average time/residue: 0.0396 time to fit residues: 4.4058 Evaluate side-chains 89 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.152653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133096 restraints weight = 4133.557| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.96 r_work: 0.3378 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3363 Z= 0.166 Angle : 0.585 5.229 4574 Z= 0.294 Chirality : 0.041 0.156 533 Planarity : 0.005 0.063 552 Dihedral : 4.529 46.765 438 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.67 % Allowed : 17.51 % Favored : 78.81 % 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: 2.13 (0.42), residues: 402 helix: 1.66 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.29 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.011 0.001 TYR A 273 PHE 0.016 0.002 PHE A 462 TRP 0.016 0.002 TRP A 285 HIS 0.002 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 3362) covalent geometry : angle 0.58527 / 0.29 ( 4572) SS BOND : bond 0.00026 / 0.02 ( 1) SS BOND : angle 0.26006 / 0.09 ( 2) hydrogen bonds : bond 0.03737 / 2.65 ( 248) hydrogen bonds : angle 4.13597 / 3.11 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.066 Fit side-chains REVERT: A 182 LYS cc_start: 0.8260 (mttt) cc_final: 0.7538 (mmmt) REVERT: A 301 ASN cc_start: 0.8269 (t0) cc_final: 0.7792 (m-40) REVERT: A 343 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8663 (tttt) outliers start: 13 outliers final: 13 residues processed: 85 average time/residue: 0.0339 time to fit residues: 3.6616 Evaluate side-chains 88 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.153768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134295 restraints weight = 4074.820| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.92 r_work: 0.3412 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3363 Z= 0.151 Angle : 0.577 5.493 4574 Z= 0.290 Chirality : 0.040 0.152 533 Planarity : 0.005 0.063 552 Dihedral : 4.503 46.991 438 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.67 % Allowed : 17.51 % Favored : 78.81 % 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: 2.16 (0.42), residues: 402 helix: 1.70 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.14 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.010 0.001 TYR A 273 PHE 0.014 0.001 PHE A 379 TRP 0.016 0.002 TRP A 285 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3362) covalent geometry : angle 0.57685 / 0.29 ( 4572) SS BOND : bond 0.00008 / 0.01 ( 1) SS BOND : angle 0.25854 / 0.09 ( 2) hydrogen bonds : bond 0.03663 / 2.60 ( 248) hydrogen bonds : angle 4.09428 / 3.08 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.070 Fit side-chains REVERT: A 223 TYR cc_start: 0.8602 (p90) cc_final: 0.8244 (p90) REVERT: A 301 ASN cc_start: 0.8201 (t0) cc_final: 0.7800 (m-40) REVERT: A 343 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8686 (tttt) outliers start: 13 outliers final: 13 residues processed: 83 average time/residue: 0.0415 time to fit residues: 4.4261 Evaluate side-chains 90 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.153190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133378 restraints weight = 4152.849| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.99 r_work: 0.3374 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3363 Z= 0.167 Angle : 0.590 5.842 4574 Z= 0.297 Chirality : 0.041 0.151 533 Planarity : 0.005 0.063 552 Dihedral : 4.506 46.749 438 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.95 % Allowed : 17.80 % Favored : 78.25 % 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: 2.18 (0.42), residues: 402 helix: 1.71 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.22 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.011 0.001 TYR A 273 PHE 0.026 0.002 PHE A 322 TRP 0.016 0.002 TRP A 285 HIS 0.002 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 3362) covalent geometry : angle 0.58994 / 0.30 ( 4572) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.25838 / 0.09 ( 2) hydrogen bonds : bond 0.03730 / 2.65 ( 248) hydrogen bonds : angle 4.12100 / 3.10 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 889.92 seconds wall clock time: 15 minutes 56.92 seconds (956.92 seconds total)