Starting phenix.real_space_refine on Tue Aug 4 16:40:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vct_64967/08_2026/9vct_64967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vct_64967/08_2026/9vct_64967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vct_64967/08_2026/9vct_64967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vct_64967/08_2026/9vct_64967.map" model { file = "/net/cci-nas-00/data/ceres_data/9vct_64967/08_2026/9vct_64967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vct_64967/08_2026/9vct_64967.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 3104 2.51 5 N 830 2.21 5 O 891 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: 4856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4828 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 32, 'TRANS': 570} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.00, per 1000 atoms: 0.21 Number of scatterers: 4856 At special positions: 0 Unit cell: (83.83, 75.53, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 2 15.00 Mg 1 11.99 O 891 8.00 N 830 7.00 C 3104 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: 0.34 Conformation dependent library (CDL) restraints added in 169.5 milliseconds 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 58.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 89 through 102 removed outlier: 3.506A pdb=" N VAL A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.677A pdb=" N GLN A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.737A pdb=" N PHE A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 5.633A pdb=" N ASP A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 192 through 198 removed outlier: 4.279A pdb=" N MET A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 4.343A pdb=" N HIS A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.546A pdb=" N ARG A 297 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 4.027A pdb=" N TRP A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 374 through 389 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.674A pdb=" N ASP A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.514A pdb=" N ILE A 427 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET A 429 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 487 through 500 removed outlier: 3.681A pdb=" N LYS A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.573A pdb=" N CYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 621 through 643 Processing helix chain 'A' and resid 651 through 672 removed outlier: 3.800A pdb=" N ASN A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.558A pdb=" N LEU A 676 " --> pdb=" O ASN A 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 272 through 275 removed outlier: 6.906A pdb=" N ALA A 288 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS A 320 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE A 290 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 317 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 319 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 321 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.489A pdb=" N SER A 352 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR A 485 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS A 369 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 423 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 448 removed outlier: 3.748A pdb=" N GLU A 457 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 508 through 510 removed outlier: 5.542A pdb=" N ALA A 508 " --> pdb=" O PHE A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 250 hydrogen bonds defined for protein. 732 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: 0.49 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: 1586 1.35 - 1.46: 1080 1.46 - 1.58: 2256 1.58 - 1.70: 4 1.70 - 1.81: 42 Bond restraints: 4968 Sorted by residual: bond pdb=" C1' ADP A 801 " pdb=" C2' ADP A 801 " ideal model delta sigma weight residual 1.524 1.300 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1' ADP A 801 " pdb=" O4' ADP A 801 " ideal model delta sigma weight residual 1.426 1.626 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C4' ADP A 801 " pdb=" O4' ADP A 801 " ideal model delta sigma weight residual 1.426 1.317 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C6 ADP A 801 " pdb=" N6 ADP A 801 " ideal model delta sigma weight residual 1.355 1.457 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 4963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 6683 3.09 - 6.18: 33 6.18 - 9.26: 11 9.26 - 12.35: 5 12.35 - 15.44: 2 Bond angle restraints: 6734 Sorted by residual: angle pdb=" N1 ADP A 801 " pdb=" C6 ADP A 801 " pdb=" N6 ADP A 801 " ideal model delta sigma weight residual 120.00 104.56 15.44 3.00e+00 1.11e-01 2.65e+01 angle pdb=" C5 ADP A 801 " pdb=" C6 ADP A 801 " pdb=" N6 ADP A 801 " ideal model delta sigma weight residual 120.00 134.94 -14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CA MET A 330 " pdb=" CB MET A 330 " pdb=" CG MET A 330 " ideal model delta sigma weight residual 114.10 123.38 -9.28 2.00e+00 2.50e-01 2.15e+01 angle pdb=" N MET A 330 " pdb=" CA MET A 330 " pdb=" CB MET A 330 " ideal model delta sigma weight residual 110.28 116.52 -6.24 1.55e+00 4.16e-01 1.62e+01 angle pdb=" C LYS A 613 " pdb=" N TRP A 614 " pdb=" CA TRP A 614 " ideal model delta sigma weight residual 121.80 130.71 -8.91 2.44e+00 1.68e-01 1.33e+01 ... (remaining 6729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.07: 2862 31.07 - 62.14: 146 62.14 - 93.21: 9 93.21 - 124.28: 2 124.28 - 155.35: 1 Dihedral angle restraints: 3020 sinusoidal: 1248 harmonic: 1772 Sorted by residual: dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 144.65 155.35 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C4' ADP A 801 " pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual 180.00 58.21 121.79 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 55.86 -115.86 1 2.00e+01 2.50e-03 3.45e+01 ... (remaining 3017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 495 0.030 - 0.061: 159 0.061 - 0.091: 54 0.091 - 0.121: 36 0.121 - 0.151: 6 Chirality restraints: 750 Sorted by residual: chirality pdb=" CB THR A 335 " pdb=" CA THR A 335 " pdb=" OG1 THR A 335 " pdb=" CG2 THR A 335 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA TRP A 614 " pdb=" N TRP A 614 " pdb=" C TRP A 614 " pdb=" CB TRP A 614 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA PRO A 323 " pdb=" N PRO A 323 " pdb=" C PRO A 323 " pdb=" CB PRO A 323 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 747 not shown) Planarity restraints: 862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 322 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO A 323 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 614 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 615 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 615 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 615 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 359 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLU A 359 " -0.022 2.00e-02 2.50e+03 pdb=" O GLU A 359 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 360 " 0.007 2.00e-02 2.50e+03 ... (remaining 859 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 241 2.73 - 3.27: 5020 3.27 - 3.81: 8337 3.81 - 4.36: 9296 4.36 - 4.90: 15761 Nonbonded interactions: 38655 Sorted by model distance: nonbonded pdb=" OG SER A 374 " pdb=" OD1 ASP A 377 " model vdw 2.181 3.040 nonbonded pdb=" NH2 ARG A 200 " pdb=" O LEU A 309 " model vdw 2.250 3.120 nonbonded pdb=" O VAL A 537 " pdb=" OG SER A 540 " model vdw 2.269 3.040 nonbonded pdb=" OG SER A 360 " pdb=" OD2 ASP A 362 " model vdw 2.276 3.040 nonbonded pdb=" O GLY A 428 " pdb=" NH2 ARG A 470 " model vdw 2.287 3.120 ... (remaining 38650 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: 1.530 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.630 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.224 4968 Z= 0.312 Angle : 0.714 15.439 6734 Z= 0.318 Chirality : 0.040 0.151 750 Planarity : 0.004 0.064 862 Dihedral : 17.932 155.354 1870 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.67 % Rotamer: Outliers : 0.19 % Allowed : 32.83 % Favored : 66.98 % 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: 1.09 (0.35), residues: 601 helix: 1.86 (0.29), residues: 331 sheet: -1.13 (0.69), residues: 63 loop : -0.46 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 569 TYR 0.011 0.001 TYR A 396 PHE 0.009 0.001 PHE A 124 TRP 0.005 0.001 TRP A 614 HIS 0.004 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.31 ( 4968) covalent geometry : angle 0.71368 / 0.32 ( 6734) hydrogen bonds : bond 0.14230 / 8.45 ( 250) hydrogen bonds : angle 5.60108 / 4.04 ( 732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.126 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.0576 time to fit residues: 5.0478 Evaluate side-chains 64 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.168089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118437 restraints weight = 8441.593| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 4.31 r_work: 0.3490 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4968 Z= 0.151 Angle : 0.611 9.003 6734 Z= 0.300 Chirality : 0.041 0.156 750 Planarity : 0.005 0.068 862 Dihedral : 9.649 164.053 666 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.67 % Rotamer: Outliers : 3.38 % Allowed : 28.71 % Favored : 67.92 % 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: 0.89 (0.34), residues: 601 helix: 1.84 (0.28), residues: 336 sheet: -1.64 (0.62), residues: 63 loop : -0.75 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 569 TYR 0.015 0.001 TYR A 396 PHE 0.013 0.001 PHE A 204 TRP 0.004 0.001 TRP A 614 HIS 0.005 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4968) covalent geometry : angle 0.61055 / 0.30 ( 6734) hydrogen bonds : bond 0.03847 / 2.40 ( 250) hydrogen bonds : angle 4.39636 / 3.18 ( 732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8445 (pmm) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 0.0408 time to fit residues: 4.1519 Evaluate side-chains 69 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 674 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.170232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119078 restraints weight = 8342.083| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 4.43 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4968 Z= 0.114 Angle : 0.582 9.011 6734 Z= 0.282 Chirality : 0.040 0.153 750 Planarity : 0.005 0.068 862 Dihedral : 9.519 173.929 666 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.33 % Favored : 97.50 % Rotamer: Outliers : 4.50 % Allowed : 28.89 % Favored : 66.60 % 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: 0.82 (0.34), residues: 601 helix: 1.80 (0.28), residues: 336 sheet: -1.76 (0.60), residues: 62 loop : -0.79 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 569 TYR 0.012 0.001 TYR A 396 PHE 0.010 0.001 PHE A 204 TRP 0.003 0.000 TRP A 614 HIS 0.007 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 4968) covalent geometry : angle 0.58188 / 0.28 ( 6734) hydrogen bonds : bond 0.03456 / 2.15 ( 250) hydrogen bonds : angle 4.10780 / 2.96 ( 732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8447 (pmm) outliers start: 24 outliers final: 11 residues processed: 75 average time/residue: 0.0424 time to fit residues: 4.4872 Evaluate side-chains 72 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 670 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.169734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118621 restraints weight = 8351.014| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.44 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4968 Z= 0.120 Angle : 0.580 8.806 6734 Z= 0.284 Chirality : 0.040 0.153 750 Planarity : 0.005 0.068 862 Dihedral : 8.762 165.907 666 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 4.88 % Allowed : 28.52 % Favored : 66.60 % 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: 0.78 (0.34), residues: 601 helix: 1.77 (0.28), residues: 336 sheet: -1.84 (0.58), residues: 63 loop : -0.78 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 569 TYR 0.013 0.001 TYR A 396 PHE 0.013 0.001 PHE A 204 TRP 0.003 0.000 TRP A 614 HIS 0.006 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 4968) covalent geometry : angle 0.58048 / 0.28 ( 6734) hydrogen bonds : bond 0.03406 / 2.12 ( 250) hydrogen bonds : angle 4.02281 / 2.89 ( 732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8387 (pmm) outliers start: 26 outliers final: 16 residues processed: 77 average time/residue: 0.0332 time to fit residues: 3.7332 Evaluate side-chains 76 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 670 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 31 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.170646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119717 restraints weight = 8407.042| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 4.41 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4968 Z= 0.110 Angle : 0.591 8.792 6734 Z= 0.286 Chirality : 0.040 0.150 750 Planarity : 0.004 0.067 862 Dihedral : 7.688 145.043 666 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.83 % Favored : 97.00 % Rotamer: Outliers : 4.32 % Allowed : 30.02 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.34), residues: 601 helix: 1.75 (0.28), residues: 336 sheet: -1.79 (0.57), residues: 63 loop : -0.77 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 569 TYR 0.012 0.001 TYR A 396 PHE 0.010 0.001 PHE A 124 TRP 0.002 0.000 TRP A 614 HIS 0.005 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4968) covalent geometry : angle 0.59110 / 0.29 ( 6734) hydrogen bonds : bond 0.03263 / 2.05 ( 250) hydrogen bonds : angle 3.99490 / 2.88 ( 732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8389 (pmm) REVERT: A 601 GLU cc_start: 0.8179 (pt0) cc_final: 0.7922 (pt0) outliers start: 23 outliers final: 14 residues processed: 74 average time/residue: 0.0422 time to fit residues: 4.4484 Evaluate side-chains 73 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 674 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.0000 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN A 523 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.171400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120796 restraints weight = 8509.014| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 4.42 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4968 Z= 0.104 Angle : 0.591 8.949 6734 Z= 0.285 Chirality : 0.040 0.146 750 Planarity : 0.004 0.067 862 Dihedral : 6.121 107.396 666 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.84 % Rotamer: Outliers : 4.13 % Allowed : 29.83 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.34), residues: 601 helix: 1.77 (0.29), residues: 336 sheet: -1.75 (0.56), residues: 63 loop : -0.76 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 569 TYR 0.011 0.001 TYR A 396 PHE 0.010 0.001 PHE A 204 TRP 0.003 0.000 TRP A 640 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 4968) covalent geometry : angle 0.59127 / 0.28 ( 6734) hydrogen bonds : bond 0.03112 / 1.97 ( 250) hydrogen bonds : angle 3.91710 / 2.80 ( 732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8959 (m-40) cc_final: 0.8623 (m-40) REVERT: A 198 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8400 (pmm) REVERT: A 295 MET cc_start: 0.7920 (mmm) cc_final: 0.7557 (mmm) REVERT: A 322 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: A 601 GLU cc_start: 0.8174 (pt0) cc_final: 0.7925 (pt0) outliers start: 22 outliers final: 9 residues processed: 75 average time/residue: 0.0466 time to fit residues: 4.9217 Evaluate side-chains 68 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 674 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.0070 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 50.0000 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.171529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.120369 restraints weight = 8343.575| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.47 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4968 Z= 0.107 Angle : 0.621 10.801 6734 Z= 0.291 Chirality : 0.040 0.164 750 Planarity : 0.004 0.067 862 Dihedral : 5.275 80.780 666 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 2.81 % Allowed : 30.77 % Favored : 66.42 % 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: 0.82 (0.34), residues: 601 helix: 1.75 (0.28), residues: 336 sheet: -1.73 (0.57), residues: 62 loop : -0.70 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 569 TYR 0.011 0.001 TYR A 396 PHE 0.010 0.001 PHE A 124 TRP 0.003 0.000 TRP A 614 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 4968) covalent geometry : angle 0.62074 / 0.29 ( 6734) hydrogen bonds : bond 0.03061 / 1.91 ( 250) hydrogen bonds : angle 3.91820 / 2.80 ( 732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8449 (pmm) REVERT: A 295 MET cc_start: 0.7923 (mmm) cc_final: 0.7565 (mmm) REVERT: A 601 GLU cc_start: 0.8129 (pt0) cc_final: 0.7854 (pt0) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.0434 time to fit residues: 4.4186 Evaluate side-chains 69 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 674 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 60.0000 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.170151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119082 restraints weight = 8542.303| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 4.46 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4968 Z= 0.123 Angle : 0.632 8.998 6734 Z= 0.299 Chirality : 0.040 0.158 750 Planarity : 0.004 0.067 862 Dihedral : 4.834 62.594 666 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 2.44 % Allowed : 30.77 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.34), residues: 601 helix: 1.75 (0.29), residues: 336 sheet: -2.10 (0.60), residues: 58 loop : -0.65 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 595 TYR 0.013 0.001 TYR A 396 PHE 0.015 0.001 PHE A 127 TRP 0.003 0.000 TRP A 614 HIS 0.002 0.000 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 4968) covalent geometry : angle 0.63206 / 0.30 ( 6734) hydrogen bonds : bond 0.03222 / 1.99 ( 250) hydrogen bonds : angle 3.97079 / 2.84 ( 732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8413 (pmm) REVERT: A 295 MET cc_start: 0.7974 (mmm) cc_final: 0.7579 (mmm) REVERT: A 322 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5975 (tm-30) REVERT: A 601 GLU cc_start: 0.8143 (pt0) cc_final: 0.7860 (pt0) outliers start: 13 outliers final: 10 residues processed: 67 average time/residue: 0.0559 time to fit residues: 5.1578 Evaluate side-chains 69 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 674 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 60.0000 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.166805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115681 restraints weight = 8385.668| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 4.38 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4968 Z= 0.180 Angle : 0.690 9.462 6734 Z= 0.332 Chirality : 0.042 0.175 750 Planarity : 0.005 0.071 862 Dihedral : 4.879 54.080 666 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 3.00 % Allowed : 30.21 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.68 (0.35), residues: 601 helix: 1.69 (0.28), residues: 336 sheet: -2.41 (0.62), residues: 58 loop : -0.67 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.019 0.002 TYR A 396 PHE 0.015 0.002 PHE A 127 TRP 0.009 0.001 TRP A 614 HIS 0.002 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 4968) covalent geometry : angle 0.69031 / 0.33 ( 6734) hydrogen bonds : bond 0.03745 / 2.27 ( 250) hydrogen bonds : angle 4.15453 / 2.98 ( 732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8367 (pmm) REVERT: A 346 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8720 (ptpp) REVERT: A 601 GLU cc_start: 0.8170 (pt0) cc_final: 0.7884 (pt0) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.0378 time to fit residues: 3.7329 Evaluate side-chains 71 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 674 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.168927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117425 restraints weight = 8414.380| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 4.45 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4968 Z= 0.136 Angle : 0.680 9.832 6734 Z= 0.322 Chirality : 0.041 0.163 750 Planarity : 0.005 0.068 862 Dihedral : 4.627 49.098 666 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 2.63 % Allowed : 30.96 % Favored : 66.42 % 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: 0.70 (0.35), residues: 601 helix: 1.74 (0.29), residues: 336 sheet: -2.49 (0.61), residues: 58 loop : -0.70 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.015 0.001 TYR A 396 PHE 0.015 0.001 PHE A 474 TRP 0.007 0.001 TRP A 614 HIS 0.002 0.000 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4968) covalent geometry : angle 0.68034 / 0.32 ( 6734) hydrogen bonds : bond 0.03448 / 2.12 ( 250) hydrogen bonds : angle 4.01101 / 2.86 ( 732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.171 Fit side-chains REVERT: A 198 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8384 (pmm) REVERT: A 331 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 601 GLU cc_start: 0.8172 (pt0) cc_final: 0.7871 (pt0) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.0569 time to fit residues: 5.3972 Evaluate side-chains 68 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 674 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 60.0000 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.172659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127623 restraints weight = 8448.617| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 4.89 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4968 Z= 0.129 Angle : 0.675 9.686 6734 Z= 0.319 Chirality : 0.041 0.158 750 Planarity : 0.005 0.072 862 Dihedral : 4.185 38.215 666 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 2.06 % Allowed : 31.33 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.35), residues: 601 helix: 1.73 (0.29), residues: 336 sheet: -2.54 (0.60), residues: 58 loop : -0.76 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.014 0.001 TYR A 396 PHE 0.011 0.001 PHE A 204 TRP 0.004 0.001 TRP A 614 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4968) covalent geometry : angle 0.67526 / 0.32 ( 6734) hydrogen bonds : bond 0.03393 / 2.11 ( 250) hydrogen bonds : angle 3.97879 / 2.83 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 955.97 seconds wall clock time: 17 minutes 6.03 seconds (1026.03 seconds total)