Starting phenix.real_space_refine on Thu Oct 22 17:59:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sh1_54886/10_2026/9sh1_54886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sh1_54886/10_2026/9sh1_54886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sh1_54886/10_2026/9sh1_54886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sh1_54886/10_2026/9sh1_54886.map" model { file = "/net/cci-nas-00/data/ceres_data/9sh1_54886/10_2026/9sh1_54886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sh1_54886/10_2026/9sh1_54886.cif" } resolution = 2.14 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= 0.072 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 9 5.16 5 C 1930 2.51 5 N 537 2.21 5 O 604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3080 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Time building chain proxies: 0.86, per 1000 atoms: 0.28 Number of scatterers: 3080 At special positions: 0 Unit cell: (80.91, 91.14, 171.12, 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 9 16.00 O 604 8.00 N 537 7.00 C 1930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 345 " 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: 0.19 Conformation dependent library (CDL) restraints added in 117.1 milliseconds 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 19.3% alpha, 56.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.899A pdb=" N LEU A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.512A pdb=" N ARG A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 93 removed outlier: 3.767A pdb=" N ALA A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.333A pdb=" N SER A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 200 through 203 removed outlier: 3.848A pdb=" N THR A 203 " --> pdb=" O LYS A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 7.737A pdb=" N SER A 3 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 42 " --> pdb=" O SER A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.673A pdb=" N ASN A 25 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE A 69 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 27 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 68 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 61 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 70 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 101 removed outlier: 3.614A pdb=" N SER A 134 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 212 Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 242 removed outlier: 4.677A pdb=" N LYS A 394 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY A 366 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 409 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE A 364 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 292 removed outlier: 3.541A pdb=" N THR A 325 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 337 174 hydrogen bonds defined for protein. 501 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: 0.45 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1041 1.34 - 1.46: 539 1.46 - 1.58: 1516 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3112 Sorted by residual: bond pdb=" CA VAL A 380 " pdb=" CB VAL A 380 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.55e-02 4.16e+03 4.80e-01 bond pdb=" C LEU A 228 " pdb=" N PRO A 229 " ideal model delta sigma weight residual 1.334 1.348 -0.014 2.34e-02 1.83e+03 3.51e-01 bond pdb=" CB VAL A 9 " pdb=" CG1 VAL A 9 " ideal model delta sigma weight residual 1.521 1.540 -0.019 3.30e-02 9.18e+02 3.18e-01 bond pdb=" CA VAL A 9 " pdb=" C VAL A 9 " ideal model delta sigma weight residual 1.523 1.530 -0.007 1.27e-02 6.20e+03 2.63e-01 bond pdb=" N ASP A 202 " pdb=" CA ASP A 202 " ideal model delta sigma weight residual 1.457 1.464 -0.006 1.29e-02 6.01e+03 2.40e-01 ... (remaining 3107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4102 1.07 - 2.14: 75 2.14 - 3.21: 20 3.21 - 4.28: 3 4.28 - 5.35: 3 Bond angle restraints: 4203 Sorted by residual: angle pdb=" C ASN A 201 " pdb=" N ASP A 202 " pdb=" CA ASP A 202 " ideal model delta sigma weight residual 121.54 125.44 -3.90 1.91e+00 2.74e-01 4.17e+00 angle pdb=" CA LEU A 392 " pdb=" CB LEU A 392 " pdb=" CG LEU A 392 " ideal model delta sigma weight residual 116.30 121.65 -5.35 3.50e+00 8.16e-02 2.34e+00 angle pdb=" N VAL A 9 " pdb=" CA VAL A 9 " pdb=" C VAL A 9 " ideal model delta sigma weight residual 109.34 106.53 2.81 2.08e+00 2.31e-01 1.83e+00 angle pdb=" CA PRO A 387 " pdb=" CB PRO A 387 " pdb=" CG PRO A 387 " ideal model delta sigma weight residual 104.50 107.05 -2.55 1.90e+00 2.77e-01 1.80e+00 angle pdb=" CB PRO A 387 " pdb=" CG PRO A 387 " pdb=" CD PRO A 387 " ideal model delta sigma weight residual 106.10 110.22 -4.12 3.20e+00 9.77e-02 1.66e+00 ... (remaining 4198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1799 17.98 - 35.97: 98 35.97 - 53.95: 22 53.95 - 71.93: 5 71.93 - 89.92: 2 Dihedral angle restraints: 1926 sinusoidal: 775 harmonic: 1151 Sorted by residual: dihedral pdb=" CA ASP A 202 " pdb=" CB ASP A 202 " pdb=" CG ASP A 202 " pdb=" OD1 ASP A 202 " ideal model delta sinusoidal sigma weight residual -30.00 -89.29 59.29 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU A 370 " pdb=" CG GLU A 370 " pdb=" CD GLU A 370 " pdb=" OE1 GLU A 370 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" N ARG A 412 " pdb=" CA ARG A 412 " pdb=" CB ARG A 412 " pdb=" CG ARG A 412 " ideal model delta sinusoidal sigma weight residual -60.00 -114.02 54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 1923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 299 0.027 - 0.054: 129 0.054 - 0.081: 33 0.081 - 0.109: 37 0.109 - 0.136: 9 Chirality restraints: 507 Sorted by residual: chirality pdb=" CA ILE A 386 " pdb=" N ILE A 386 " pdb=" C ILE A 386 " pdb=" CB ILE A 386 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 323 " pdb=" N ILE A 323 " pdb=" C ILE A 323 " pdb=" CB ILE A 323 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 409 " pdb=" N ILE A 409 " pdb=" C ILE A 409 " pdb=" CB ILE A 409 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 504 not shown) Planarity restraints: 542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 386 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 387 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 43 " 0.013 5.00e-02 4.00e+02 2.01e-02 6.48e-01 pdb=" N PRO A 44 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 70 " 0.011 5.00e-02 4.00e+02 1.74e-02 4.85e-01 pdb=" N PRO A 71 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.010 5.00e-02 4.00e+02 ... (remaining 539 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 614 2.80 - 3.32: 2651 3.32 - 3.85: 4600 3.85 - 4.37: 5005 4.37 - 4.90: 9176 Nonbonded interactions: 22046 Sorted by model distance: nonbonded pdb=" O GLY A 93 " pdb=" NH2 ARG A 132 " model vdw 2.274 3.120 nonbonded pdb=" O ASP A 91 " pdb=" NH1 ARG A 132 " model vdw 2.369 3.120 nonbonded pdb=" O PRO A 387 " pdb=" N ILE A 389 " model vdw 2.421 3.120 nonbonded pdb=" NZ LYS A 105 " pdb=" OE1 GLU A 109 " model vdw 2.433 3.120 nonbonded pdb=" OG1 THR A 141 " pdb=" OG1 THR A 143 " model vdw 2.506 3.040 ... (remaining 22041 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: 2.360 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.700 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: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.001 0.019 3113 Z= 0.080 Angle : 0.422 5.352 4205 Z= 0.221 Chirality : 0.041 0.136 507 Planarity : 0.003 0.041 542 Dihedral : 12.360 89.918 1177 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.76 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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 (0.43), residues: 398 helix: 1.80 (0.67), residues: 66 sheet: 0.80 (0.37), residues: 208 loop : -0.62 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.006 0.001 TYR A 96 PHE 0.003 0.000 PHE A 100 TRP 0.001 0.000 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00150 / 0.08 ( 3112) covalent geometry : angle 0.42205 / 0.22 ( 4203) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 0.15658 / 0.09 ( 2) hydrogen bonds : bond 0.19406 / 12.18 ( 174) hydrogen bonds : angle 7.69642 / 5.52 ( 501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 157 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7314 (ttp80) REVERT: A 349 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7438 (ttmt) outliers start: 0 outliers final: 1 residues processed: 113 average time/residue: 0.6761 time to fit residues: 77.9318 Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.173969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147117 restraints weight = 4095.842| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.97 r_work: 0.4022 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3113 Z= 0.166 Angle : 0.587 7.401 4205 Z= 0.304 Chirality : 0.044 0.138 507 Planarity : 0.004 0.041 542 Dihedral : 4.069 22.024 426 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.76 % Favored : 96.98 % Rotamer: Outliers : 2.05 % Allowed : 14.62 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.42), residues: 398 helix: 1.42 (0.65), residues: 69 sheet: 0.59 (0.35), residues: 208 loop : -0.82 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 185 TYR 0.011 0.001 TYR A 96 PHE 0.008 0.001 PHE A 408 TRP 0.008 0.001 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 3112) covalent geometry : angle 0.58695 / 0.30 ( 4203) SS BOND : bond 0.00198 / 0.10 ( 1) SS BOND : angle 0.85246 / 0.47 ( 2) hydrogen bonds : bond 0.03229 / 2.00 ( 174) hydrogen bonds : angle 5.46448 / 3.86 ( 501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7158 (tmm) cc_final: 0.6892 (tmm) REVERT: A 61 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7179 (ttm-80) REVERT: A 132 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7749 (ttp-170) REVERT: A 371 GLU cc_start: 0.8107 (tt0) cc_final: 0.7847 (tt0) outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 0.6758 time to fit residues: 73.6958 Evaluate side-chains 102 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [25, 37, 14, 3, 13, 26, 1, 38, 8, 35, 19] chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.170260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.143181 restraints weight = 4059.840| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.98 r_work: 0.3964 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3113 Z= 0.232 Angle : 0.606 7.142 4205 Z= 0.311 Chirality : 0.045 0.137 507 Planarity : 0.004 0.039 542 Dihedral : 4.373 17.241 424 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.02 % Favored : 96.73 % Rotamer: Outliers : 2.92 % Allowed : 14.62 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.40), residues: 398 helix: 1.17 (0.63), residues: 69 sheet: 0.39 (0.34), residues: 202 loop : -1.02 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 132 TYR 0.009 0.002 TYR A 96 PHE 0.013 0.001 PHE A 408 TRP 0.010 0.002 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 3112) covalent geometry : angle 0.60629 / 0.31 ( 4203) SS BOND : bond 0.00249 / 0.13 ( 1) SS BOND : angle 0.66918 / 0.37 ( 2) hydrogen bonds : bond 0.03214 / 2.00 ( 174) hydrogen bonds : angle 5.48592 / 3.89 ( 501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7303 (tmm) cc_final: 0.7097 (tmm) REVERT: A 67 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7662 (m) REVERT: A 132 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7720 (ttp-110) REVERT: A 219 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8151 (mmpt) outliers start: 10 outliers final: 3 residues processed: 100 average time/residue: 0.6651 time to fit residues: 67.8427 Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [6, 2, 20, 21, 7, 39, 18, 15, 19, 36, 4] chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 21 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.0050 chunk 4 optimal weight: 1.9990 overall best weight: 0.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.173359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.146466 restraints weight = 4023.272| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.96 r_work: 0.3994 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3113 Z= 0.143 Angle : 0.570 7.208 4205 Z= 0.293 Chirality : 0.044 0.141 507 Planarity : 0.003 0.036 542 Dihedral : 4.124 17.810 424 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.02 % Favored : 96.73 % Rotamer: Outliers : 2.34 % Allowed : 18.42 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.12 (0.41), residues: 398 helix: 1.30 (0.62), residues: 69 sheet: 0.39 (0.34), residues: 207 loop : -1.07 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 61 TYR 0.003 0.001 TYR A 283 PHE 0.010 0.001 PHE A 408 TRP 0.008 0.001 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3112) covalent geometry : angle 0.56990 / 0.29 ( 4203) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.50439 / 0.29 ( 2) hydrogen bonds : bond 0.02706 / 1.72 ( 174) hydrogen bonds : angle 5.12447 / 3.63 ( 501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.098 Fit side-chains REVERT: A 61 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7453 (tpp80) REVERT: A 67 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7447 (m) REVERT: A 132 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7265 (ttp-110) REVERT: A 219 LYS cc_start: 0.8636 (mtpt) cc_final: 0.7598 (tmtp) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.6545 time to fit residues: 66.1830 Evaluate side-chains 105 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 410 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [8, 14, 5, 27, 37, 38, 22, 4, 13, 30, 36] chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 38 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN A 54 GLN A 84 GLN A 101 GLN A 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.171278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.144421 restraints weight = 3951.039| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.95 r_work: 0.3980 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3113 Z= 0.170 Angle : 0.591 8.166 4205 Z= 0.299 Chirality : 0.044 0.141 507 Planarity : 0.003 0.034 542 Dihedral : 4.230 17.690 424 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.27 % Favored : 96.48 % Rotamer: Outliers : 3.51 % Allowed : 19.88 % Favored : 76.61 % 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: -0.01 (0.41), residues: 398 helix: 0.82 (0.61), residues: 75 sheet: 0.35 (0.35), residues: 202 loop : -1.01 (0.53), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 175 TYR 0.004 0.001 TYR A 369 PHE 0.010 0.001 PHE A 408 TRP 0.008 0.001 TRP A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 3112) covalent geometry : angle 0.59062 / 0.30 ( 4203) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 0.49201 / 0.28 ( 2) hydrogen bonds : bond 0.02718 / 1.72 ( 174) hydrogen bonds : angle 5.11267 / 3.63 ( 501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8126 (tm-30) REVERT: A 60 MET cc_start: 0.7227 (tmm) cc_final: 0.6526 (tmm) REVERT: A 61 ARG cc_start: 0.7866 (tpp-160) cc_final: 0.7359 (tpp-160) REVERT: A 132 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7747 (ttp-110) REVERT: A 185 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7922 (ttp80) REVERT: A 219 LYS cc_start: 0.8646 (mtpt) cc_final: 0.7627 (tmtt) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.6825 time to fit residues: 73.7674 Evaluate side-chains 107 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [39, 36, 8, 2, 6, 25, 15, 0, 18, 14, 19] chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 101 GLN A 329 ASN A 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.169614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.142903 restraints weight = 3990.583| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.95 r_work: 0.3961 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3113 Z= 0.241 Angle : 0.637 6.426 4205 Z= 0.323 Chirality : 0.045 0.142 507 Planarity : 0.004 0.034 542 Dihedral : 4.504 17.840 424 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.77 % Favored : 95.98 % Rotamer: Outliers : 3.51 % Allowed : 20.47 % Favored : 76.02 % 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: 0.06 (0.41), residues: 398 helix: 0.74 (0.61), residues: 74 sheet: 0.39 (0.33), residues: 228 loop : -1.15 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 132 TYR 0.005 0.001 TYR A 283 PHE 0.012 0.001 PHE A 408 TRP 0.009 0.002 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 ( 3112) covalent geometry : angle 0.63664 / 0.32 ( 4203) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 0.54845 / 0.31 ( 2) hydrogen bonds : bond 0.02948 / 1.86 ( 174) hydrogen bonds : angle 5.32981 / 3.78 ( 501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.121 Fit side-chains REVERT: A 16 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8145 (tm-30) REVERT: A 61 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7374 (tpp80) REVERT: A 132 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7798 (ttp-110) REVERT: A 204 SER cc_start: 0.6470 (t) cc_final: 0.6133 (m) REVERT: A 219 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8163 (mmpt) outliers start: 12 outliers final: 6 residues processed: 107 average time/residue: 0.6642 time to fit residues: 72.5298 Evaluate side-chains 106 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [5, 24, 26, 34, 31, 23, 37, 17, 6, 10, 36] chunk 5 optimal weight: 0.0270 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 101 GLN A 329 ASN A 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.170486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.143834 restraints weight = 4032.664| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.98 r_work: 0.3973 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3113 Z= 0.192 Angle : 0.643 10.294 4205 Z= 0.321 Chirality : 0.044 0.141 507 Planarity : 0.004 0.038 542 Dihedral : 4.490 17.660 424 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.27 % Favored : 96.48 % Rotamer: Outliers : 4.09 % Allowed : 18.71 % Favored : 77.19 % 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: -0.00 (0.41), residues: 398 helix: 0.76 (0.61), residues: 74 sheet: 0.48 (0.34), residues: 217 loop : -1.43 (0.54), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.008 0.002 TYR A 96 PHE 0.016 0.002 PHE A 393 TRP 0.009 0.001 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 3112) covalent geometry : angle 0.64264 / 0.32 ( 4203) SS BOND : bond 0.00128 / 0.07 ( 1) SS BOND : angle 0.48978 / 0.28 ( 2) hydrogen bonds : bond 0.02765 / 1.74 ( 174) hydrogen bonds : angle 5.21383 / 3.70 ( 501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.094 Fit side-chains REVERT: A 16 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8128 (tm-30) REVERT: A 60 MET cc_start: 0.7212 (tmm) cc_final: 0.6820 (tmm) REVERT: A 61 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7237 (tpp80) REVERT: A 132 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7604 (mtp180) REVERT: A 204 SER cc_start: 0.6435 (t) cc_final: 0.6097 (m) outliers start: 14 outliers final: 9 residues processed: 106 average time/residue: 0.6792 time to fit residues: 73.3634 Evaluate side-chains 109 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [18, 6, 39, 9, 33, 38, 37, 0, 31, 10, 28] chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 38 optimal weight: 0.2980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.0270 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 101 GLN A 329 ASN A 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.170668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.144208 restraints weight = 4100.166| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.00 r_work: 0.3980 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3113 Z= 0.163 Angle : 0.645 8.126 4205 Z= 0.328 Chirality : 0.044 0.149 507 Planarity : 0.004 0.044 542 Dihedral : 4.462 18.152 424 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.76 % Favored : 96.98 % Rotamer: Outliers : 2.63 % Allowed : 21.35 % Favored : 76.02 % 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: 0.00 (0.41), residues: 398 helix: 0.87 (0.61), residues: 74 sheet: 0.45 (0.34), residues: 217 loop : -1.42 (0.55), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 403 TYR 0.010 0.001 TYR A 96 PHE 0.015 0.001 PHE A 393 TRP 0.008 0.001 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3112) covalent geometry : angle 0.64526 / 0.33 ( 4203) SS BOND : bond 0.00097 / 0.05 ( 1) SS BOND : angle 0.44958 / 0.26 ( 2) hydrogen bonds : bond 0.02606 / 1.66 ( 174) hydrogen bonds : angle 5.09316 / 3.61 ( 501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.116 Fit side-chains REVERT: A 16 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8119 (tm-30) REVERT: A 60 MET cc_start: 0.7188 (tmm) cc_final: 0.6806 (tmm) REVERT: A 61 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7189 (tpp80) REVERT: A 132 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7328 (ttp-110) REVERT: A 204 SER cc_start: 0.6428 (t) cc_final: 0.6099 (m) REVERT: A 219 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8171 (mmpt) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.6847 time to fit residues: 71.9527 Evaluate side-chains 107 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [39, 24, 36, 14, 12, 1, 8, 7, 23, 15, 25] chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 14 optimal weight: 0.0770 chunk 12 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 101 GLN A 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.170123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.143661 restraints weight = 4071.938| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.99 r_work: 0.3969 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3113 Z= 0.199 Angle : 0.666 7.496 4205 Z= 0.337 Chirality : 0.044 0.142 507 Planarity : 0.004 0.044 542 Dihedral : 4.589 20.999 424 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.77 % Favored : 95.98 % Rotamer: Outliers : 2.92 % Allowed : 21.05 % Favored : 76.02 % 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: -0.04 (0.41), residues: 398 helix: 0.68 (0.61), residues: 75 sheet: 0.46 (0.34), residues: 217 loop : -1.45 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.013 0.002 TYR A 96 PHE 0.014 0.002 PHE A 393 TRP 0.008 0.001 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 3112) covalent geometry : angle 0.66643 / 0.34 ( 4203) SS BOND : bond 0.00120 / 0.06 ( 1) SS BOND : angle 0.48978 / 0.28 ( 2) hydrogen bonds : bond 0.02735 / 1.72 ( 174) hydrogen bonds : angle 5.17150 / 3.68 ( 501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8437 (tp-100) cc_final: 0.8120 (tm-30) REVERT: A 60 MET cc_start: 0.7081 (tmm) cc_final: 0.6652 (tmm) REVERT: A 61 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.7140 (tpp80) REVERT: A 132 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7669 (mtm110) REVERT: A 204 SER cc_start: 0.6462 (t) cc_final: 0.6146 (m) REVERT: A 219 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8189 (mmpt) REVERT: A 262 LYS cc_start: 0.8388 (tmtt) cc_final: 0.8186 (tmtt) outliers start: 10 outliers final: 9 residues processed: 104 average time/residue: 0.6693 time to fit residues: 70.9881 Evaluate side-chains 109 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [20, 16, 7, 21, 26, 2, 18, 17, 9, 27, 33] chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.0770 chunk 33 optimal weight: 0.4980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 84 GLN A 101 GLN A 329 ASN A 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.168177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.141996 restraints weight = 3987.707| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.98 r_work: 0.3962 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3113 Z= 0.229 Angle : 0.701 7.577 4205 Z= 0.355 Chirality : 0.045 0.137 507 Planarity : 0.005 0.050 542 Dihedral : 4.674 20.409 424 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.77 % Favored : 95.98 % Rotamer: Outliers : 2.92 % Allowed : 21.93 % Favored : 75.15 % 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: -0.13 (0.41), residues: 398 helix: 0.65 (0.61), residues: 75 sheet: 0.39 (0.34), residues: 217 loop : -1.49 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.013 0.002 TYR A 96 PHE 0.013 0.002 PHE A 393 TRP 0.008 0.001 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 ( 3112) covalent geometry : angle 0.70062 / 0.36 ( 4203) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.52100 / 0.30 ( 2) hydrogen bonds : bond 0.02816 / 1.78 ( 174) hydrogen bonds : angle 5.23165 / 3.70 ( 501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8439 (tp-100) cc_final: 0.8121 (tm-30) REVERT: A 60 MET cc_start: 0.7155 (tmm) cc_final: 0.6725 (tmm) REVERT: A 61 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7160 (tpp80) REVERT: A 132 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7700 (mtm110) REVERT: A 204 SER cc_start: 0.6501 (t) cc_final: 0.6189 (m) REVERT: A 219 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8194 (mmpt) REVERT: A 262 LYS cc_start: 0.8411 (tmtt) cc_final: 0.8204 (tmtt) outliers start: 10 outliers final: 7 residues processed: 104 average time/residue: 0.6854 time to fit residues: 72.6562 Evaluate side-chains 108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [33, 23, 19, 11, 34, 6, 36, 35, 7, 27, 20] chunk 33 optimal weight: 0.0980 chunk 23 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.0670 chunk 20 optimal weight: 0.0270 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.169950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.144194 restraints weight = 4053.002| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.95 r_work: 0.3987 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3113 Z= 0.148 Angle : 0.657 7.323 4205 Z= 0.335 Chirality : 0.044 0.141 507 Planarity : 0.004 0.048 542 Dihedral : 4.421 19.825 424 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.77 % Favored : 95.98 % Rotamer: Outliers : 2.05 % Allowed : 23.10 % Favored : 74.85 % 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: 0.02 (0.41), residues: 398 helix: 0.96 (0.62), residues: 75 sheet: 0.42 (0.34), residues: 217 loop : -1.40 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.008 0.001 TYR A 96 PHE 0.013 0.001 PHE A 393 TRP 0.007 0.001 TRP A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3112) covalent geometry : angle 0.65716 / 0.34 ( 4203) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 0.43148 / 0.25 ( 2) hydrogen bonds : bond 0.02517 / 1.61 ( 174) hydrogen bonds : angle 4.92444 / 3.49 ( 501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3591.25 seconds wall clock time: 61 minutes 34.90 seconds (3694.90 seconds total)