Starting phenix.real_space_refine on Tue Aug 4 15:54:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rh4_53957/08_2026/9rh4_53957.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rh4_53957/08_2026/9rh4_53957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rh4_53957/08_2026/9rh4_53957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rh4_53957/08_2026/9rh4_53957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rh4_53957/08_2026/9rh4_53957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rh4_53957/08_2026/9rh4_53957.map" } resolution = 3.1 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= 0.002 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 19 5.16 5 C 2965 2.51 5 N 740 2.21 5 O 826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 4550 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2827 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 15, 'TRANS': 362} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Time building chain proxies: 1.00, per 1000 atoms: 0.22 Number of scatterers: 4550 At special positions: 0 Unit cell: (68.634, 77.004, 101.277, 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 19 16.00 O 826 8.00 N 740 7.00 C 2965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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: 0.23 Conformation dependent library (CDL) restraints added in 187.4 milliseconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 7 sheets defined 52.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 removed outlier: 4.209A pdb=" N GLY A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 90 through 117 removed outlier: 4.844A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.534A pdb=" N VAL A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.978A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.099A pdb=" N GLU A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.890A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.751A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.867A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 382 removed outlier: 3.655A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.788A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.402A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.803A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS B 98 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.795A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 819 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: 0.74 Time building geometry restraints manager: 0.37 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: 1417 1.34 - 1.46: 1110 1.46 - 1.58: 2092 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4650 Sorted by residual: bond pdb=" N PRO A 120 " pdb=" CD PRO A 120 " ideal model delta sigma weight residual 1.473 1.504 -0.031 1.40e-02 5.10e+03 5.06e+00 bond pdb=" C ASP A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.15e+00 bond pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 1.471 1.455 0.016 1.32e-02 5.74e+03 1.44e+00 bond pdb=" CG PRO C 95 " pdb=" CD PRO C 95 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 8.93e-01 bond pdb=" C PRO A 120 " pdb=" O PRO A 120 " ideal model delta sigma weight residual 1.238 1.247 -0.010 1.24e-02 6.50e+03 6.34e-01 ... (remaining 4645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 6172 1.32 - 2.64: 121 2.64 - 3.96: 20 3.96 - 5.28: 11 5.28 - 6.59: 3 Bond angle restraints: 6327 Sorted by residual: angle pdb=" C GLU B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 123.15 118.89 4.26 1.21e+00 6.83e-01 1.24e+01 angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 113.47 110.02 3.45 1.01e+00 9.80e-01 1.16e+01 angle pdb=" O ASP A 119 " pdb=" C ASP A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 121.23 118.70 2.53 8.10e-01 1.52e+00 9.74e+00 angle pdb=" N THR C 7 " pdb=" CA THR C 7 " pdb=" C THR C 7 " ideal model delta sigma weight residual 109.81 115.74 -5.93 2.21e+00 2.05e-01 7.20e+00 angle pdb=" CA ASP A 119 " pdb=" C ASP A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 119.42 121.97 -2.55 1.04e+00 9.25e-01 6.02e+00 ... (remaining 6322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 2449 16.34 - 32.68: 213 32.68 - 49.02: 46 49.02 - 65.36: 14 65.36 - 81.70: 2 Dihedral angle restraints: 2724 sinusoidal: 1010 harmonic: 1714 Sorted by residual: dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 64.55 28.45 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 64.80 28.20 1 1.00e+01 1.00e-02 1.14e+01 ... (remaining 2721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 519 0.031 - 0.062: 156 0.062 - 0.093: 51 0.093 - 0.124: 22 0.124 - 0.156: 3 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA THR C 7 " pdb=" N THR C 7 " pdb=" C THR C 7 " pdb=" CB THR C 7 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL C 58 " pdb=" N VAL C 58 " pdb=" C VAL C 58 " pdb=" CB VAL C 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 748 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO C 95 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 264 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 265 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 58 " 0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO C 59 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " 0.014 5.00e-02 4.00e+02 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 575 2.75 - 3.29: 4387 3.29 - 3.83: 7596 3.83 - 4.36: 8864 4.36 - 4.90: 15676 Nonbonded interactions: 37098 Sorted by model distance: nonbonded pdb=" O TRP B 47 " pdb=" ND2 ASN B 61 " model vdw 2.217 3.120 nonbonded pdb=" OD1 ASP C 55 " pdb=" N SER C 56 " model vdw 2.292 3.120 nonbonded pdb=" OD2 ASP B 104 " pdb=" OG SER C 34 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR A 38 " pdb=" O PHE A 269 " model vdw 2.346 3.040 nonbonded pdb=" NE2 GLN A 327 " pdb=" OH TYR C 32 " model vdw 2.381 3.120 ... (remaining 37093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.840 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: 0.020 Set scattering table: 0.020 Process input model: 5.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4652 Z= 0.119 Angle : 0.526 6.594 6331 Z= 0.296 Chirality : 0.037 0.156 751 Planarity : 0.003 0.029 779 Dihedral : 13.410 81.704 1626 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.30 (0.35), residues: 596 helix: 1.35 (0.29), residues: 284 sheet: 0.99 (0.47), residues: 121 loop : 0.21 (0.51), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.011 0.001 TYR C 49 PHE 0.007 0.001 PHE A 72 TRP 0.010 0.001 TRP A 309 HIS 0.001 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 4650) covalent geometry : angle 0.52585 / 0.30 ( 6327) SS BOND : bond 0.00169 / 0.08 ( 2) SS BOND : angle 0.25721 / 0.22 ( 4) hydrogen bonds : bond 0.22011 / 14.98 ( 281) hydrogen bonds : angle 8.13788 / 5.82 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0865 time to fit residues: 7.5037 Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 116 ASN A 177 ASN B 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.172751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.115073 restraints weight = 5207.901| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.34 r_work: 0.2892 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4652 Z= 0.120 Angle : 0.532 6.000 6331 Z= 0.275 Chirality : 0.039 0.150 751 Planarity : 0.004 0.030 779 Dihedral : 4.105 18.547 641 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.28 % Allowed : 7.88 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.95 (0.35), residues: 596 helix: 2.20 (0.30), residues: 283 sheet: 1.16 (0.47), residues: 117 loop : 0.10 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.014 0.001 TYR C 49 PHE 0.009 0.001 PHE A 72 TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4650) covalent geometry : angle 0.53192 / 0.27 ( 6327) SS BOND : bond 0.00539 / 0.26 ( 2) SS BOND : angle 0.97127 / 0.76 ( 4) hydrogen bonds : bond 0.04440 / 3.06 ( 281) hydrogen bonds : angle 5.38560 / 3.94 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.110 Fit side-chains REVERT: A 92 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7931 (tmt170) REVERT: C 60 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6954 (mmmt) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.0562 time to fit residues: 5.1469 Evaluate side-chains 72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.172369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115440 restraints weight = 5189.818| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.26 r_work: 0.2823 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4652 Z= 0.171 Angle : 0.555 5.980 6331 Z= 0.284 Chirality : 0.041 0.156 751 Planarity : 0.004 0.026 779 Dihedral : 4.282 19.683 641 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.07 % Allowed : 9.34 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.77 (0.35), residues: 596 helix: 2.10 (0.30), residues: 283 sheet: 0.95 (0.47), residues: 121 loop : -0.02 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.014 0.001 TYR C 49 PHE 0.012 0.002 PHE A 72 TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 ( 4650) covalent geometry : angle 0.55417 / 0.28 ( 6327) SS BOND : bond 0.00529 / 0.25 ( 2) SS BOND : angle 1.00697 / 0.74 ( 4) hydrogen bonds : bond 0.04500 / 3.08 ( 281) hydrogen bonds : angle 5.22109 / 3.85 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.163 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 71 average time/residue: 0.0596 time to fit residues: 5.4322 Evaluate side-chains 73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117918 restraints weight = 5238.040| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.32 r_work: 0.2865 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4652 Z= 0.100 Angle : 0.480 6.011 6331 Z= 0.248 Chirality : 0.039 0.154 751 Planarity : 0.003 0.025 779 Dihedral : 4.037 17.284 641 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.87 % Allowed : 10.37 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.35), residues: 596 helix: 2.35 (0.30), residues: 283 sheet: 1.05 (0.47), residues: 120 loop : 0.12 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.010 0.001 TYR C 49 PHE 0.007 0.001 PHE A 72 TRP 0.010 0.001 TRP A 216 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 4650) covalent geometry : angle 0.47950 / 0.25 ( 6327) SS BOND : bond 0.00413 / 0.20 ( 2) SS BOND : angle 0.63976 / 0.51 ( 4) hydrogen bonds : bond 0.03554 / 2.46 ( 281) hydrogen bonds : angle 4.91031 / 3.64 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.093 Fit side-chains REVERT: A 92 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7874 (tmt170) REVERT: A 116 ASN cc_start: 0.8784 (m-40) cc_final: 0.8567 (m110) REVERT: B 60 TYR cc_start: 0.7710 (m-80) cc_final: 0.7411 (m-80) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.0492 time to fit residues: 4.6924 Evaluate side-chains 74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116714 restraints weight = 5183.500| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.16 r_work: 0.2957 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4652 Z= 0.106 Angle : 0.483 6.014 6331 Z= 0.248 Chirality : 0.039 0.154 751 Planarity : 0.003 0.025 779 Dihedral : 4.002 17.291 641 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.70 % Allowed : 9.75 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.35), residues: 596 helix: 2.43 (0.30), residues: 283 sheet: 1.06 (0.47), residues: 120 loop : 0.12 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.011 0.001 TYR C 49 PHE 0.008 0.001 PHE A 72 TRP 0.009 0.001 TRP B 47 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4650) covalent geometry : angle 0.48290 / 0.25 ( 6327) SS BOND : bond 0.00433 / 0.21 ( 2) SS BOND : angle 0.69683 / 0.55 ( 4) hydrogen bonds : bond 0.03522 / 2.43 ( 281) hydrogen bonds : angle 4.86152 / 3.61 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.140 Fit side-chains REVERT: A 92 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7883 (tmt170) REVERT: A 116 ASN cc_start: 0.8776 (m-40) cc_final: 0.8551 (m110) REVERT: B 60 TYR cc_start: 0.7696 (m-80) cc_final: 0.7390 (m-80) outliers start: 13 outliers final: 11 residues processed: 74 average time/residue: 0.0541 time to fit residues: 5.1270 Evaluate side-chains 76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 20.0000 chunk 39 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.172994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116115 restraints weight = 5272.706| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.20 r_work: 0.2898 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4652 Z= 0.112 Angle : 0.487 6.026 6331 Z= 0.249 Chirality : 0.039 0.169 751 Planarity : 0.003 0.025 779 Dihedral : 3.973 17.202 641 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.90 % Allowed : 9.75 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.35), residues: 596 helix: 2.45 (0.30), residues: 283 sheet: 1.10 (0.47), residues: 120 loop : 0.08 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.011 0.001 TYR C 49 PHE 0.009 0.001 PHE C 62 TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 4650) covalent geometry : angle 0.48649 / 0.25 ( 6327) SS BOND : bond 0.00408 / 0.20 ( 2) SS BOND : angle 0.69583 / 0.56 ( 4) hydrogen bonds : bond 0.03544 / 2.45 ( 281) hydrogen bonds : angle 4.83930 / 3.60 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.090 Fit side-chains REVERT: A 92 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7936 (tmt170) REVERT: A 379 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.7377 (m100) REVERT: B 60 TYR cc_start: 0.7763 (m-80) cc_final: 0.7444 (m-80) REVERT: C 73 LEU cc_start: 0.6698 (tp) cc_final: 0.6460 (tp) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.0470 time to fit residues: 4.4812 Evaluate side-chains 75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115905 restraints weight = 5159.822| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.14 r_work: 0.2908 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4652 Z= 0.119 Angle : 0.493 6.033 6331 Z= 0.252 Chirality : 0.039 0.166 751 Planarity : 0.003 0.026 779 Dihedral : 3.980 17.157 641 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.70 % Allowed : 10.37 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.35), residues: 596 helix: 2.43 (0.30), residues: 283 sheet: 1.14 (0.47), residues: 120 loop : 0.05 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.012 0.001 TYR C 49 PHE 0.010 0.001 PHE C 62 TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 4650) covalent geometry : angle 0.49244 / 0.25 ( 6327) SS BOND : bond 0.00389 / 0.19 ( 2) SS BOND : angle 0.71198 / 0.57 ( 4) hydrogen bonds : bond 0.03597 / 2.48 ( 281) hydrogen bonds : angle 4.83644 / 3.60 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.158 Fit side-chains REVERT: A 92 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7938 (tmt170) REVERT: A 379 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7374 (m100) REVERT: B 60 TYR cc_start: 0.7817 (m-80) cc_final: 0.7524 (m-80) REVERT: C 62 PHE cc_start: 0.7421 (m-80) cc_final: 0.7034 (m-10) REVERT: C 73 LEU cc_start: 0.6726 (tp) cc_final: 0.6500 (tp) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.0627 time to fit residues: 5.8031 Evaluate side-chains 75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.0060 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.173931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116885 restraints weight = 5222.696| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.36 r_work: 0.2882 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4652 Z= 0.099 Angle : 0.476 6.194 6331 Z= 0.244 Chirality : 0.038 0.164 751 Planarity : 0.003 0.026 779 Dihedral : 3.886 16.957 641 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.49 % Allowed : 11.41 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.35), residues: 596 helix: 2.47 (0.30), residues: 286 sheet: 1.36 (0.49), residues: 109 loop : 0.05 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.010 0.001 TYR C 49 PHE 0.010 0.001 PHE C 62 TRP 0.010 0.001 TRP A 216 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 4650) covalent geometry : angle 0.47559 / 0.24 ( 6327) SS BOND : bond 0.00335 / 0.16 ( 2) SS BOND : angle 0.54843 / 0.44 ( 4) hydrogen bonds : bond 0.03350 / 2.34 ( 281) hydrogen bonds : angle 4.74703 / 3.53 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.164 Fit side-chains REVERT: A 78 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 379 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.7327 (m100) REVERT: B 60 TYR cc_start: 0.7715 (m-80) cc_final: 0.7407 (m-80) REVERT: C 60 LYS cc_start: 0.6932 (mmmm) cc_final: 0.5926 (mmtm) REVERT: C 62 PHE cc_start: 0.7357 (m-80) cc_final: 0.7029 (m-10) outliers start: 12 outliers final: 10 residues processed: 72 average time/residue: 0.0741 time to fit residues: 6.6899 Evaluate side-chains 73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.173870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116406 restraints weight = 5185.871| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.39 r_work: 0.2872 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4652 Z= 0.105 Angle : 0.482 6.153 6331 Z= 0.245 Chirality : 0.038 0.163 751 Planarity : 0.003 0.027 779 Dihedral : 3.875 16.843 641 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.70 % Allowed : 11.20 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.35), residues: 596 helix: 2.46 (0.30), residues: 286 sheet: 1.41 (0.49), residues: 109 loop : 0.02 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.010 0.001 TYR C 49 PHE 0.008 0.001 PHE C 62 TRP 0.010 0.001 TRP B 47 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4650) covalent geometry : angle 0.48168 / 0.25 ( 6327) SS BOND : bond 0.00348 / 0.17 ( 2) SS BOND : angle 0.63846 / 0.53 ( 4) hydrogen bonds : bond 0.03394 / 2.36 ( 281) hydrogen bonds : angle 4.73803 / 3.53 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.132 Fit side-chains REVERT: A 78 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 379 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.7283 (m100) REVERT: B 60 TYR cc_start: 0.7644 (m-80) cc_final: 0.7335 (m-80) REVERT: C 60 LYS cc_start: 0.6861 (mmmm) cc_final: 0.5889 (mmtm) REVERT: C 62 PHE cc_start: 0.7320 (m-80) cc_final: 0.7014 (m-10) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.0559 time to fit residues: 5.0864 Evaluate side-chains 75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.0370 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117057 restraints weight = 5176.302| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.40 r_work: 0.3004 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4652 Z= 0.100 Angle : 0.479 6.228 6331 Z= 0.244 Chirality : 0.038 0.163 751 Planarity : 0.003 0.027 779 Dihedral : 3.842 16.717 641 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.49 % Allowed : 11.00 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.35), residues: 596 helix: 2.48 (0.30), residues: 286 sheet: 1.47 (0.49), residues: 109 loop : 0.06 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.010 0.001 TYR C 49 PHE 0.009 0.001 PHE C 62 TRP 0.013 0.001 TRP B 47 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 4650) covalent geometry : angle 0.47918 / 0.24 ( 6327) SS BOND : bond 0.00327 / 0.16 ( 2) SS BOND : angle 0.57964 / 0.48 ( 4) hydrogen bonds : bond 0.03331 / 2.33 ( 281) hydrogen bonds : angle 4.71308 / 3.51 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.152 Fit side-chains REVERT: A 78 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 379 TRP cc_start: 0.7775 (OUTLIER) cc_final: 0.7303 (m100) REVERT: B 60 TYR cc_start: 0.7616 (m-80) cc_final: 0.7317 (m-80) REVERT: C 60 LYS cc_start: 0.6859 (mmmm) cc_final: 0.5906 (mmtm) REVERT: C 62 PHE cc_start: 0.7243 (m-80) cc_final: 0.6954 (m-10) outliers start: 12 outliers final: 11 residues processed: 70 average time/residue: 0.0699 time to fit residues: 6.2587 Evaluate side-chains 74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.173947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116485 restraints weight = 5245.223| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.42 r_work: 0.2875 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4652 Z= 0.116 Angle : 0.489 6.091 6331 Z= 0.248 Chirality : 0.039 0.163 751 Planarity : 0.003 0.027 779 Dihedral : 3.867 16.540 641 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.49 % Allowed : 11.00 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.35), residues: 596 helix: 2.45 (0.30), residues: 286 sheet: 1.47 (0.50), residues: 109 loop : 0.04 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.012 0.001 TYR C 49 PHE 0.009 0.001 PHE A 72 TRP 0.013 0.001 TRP B 47 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4650) covalent geometry : angle 0.48883 / 0.25 ( 6327) SS BOND : bond 0.00327 / 0.16 ( 2) SS BOND : angle 0.67964 / 0.56 ( 4) hydrogen bonds : bond 0.03464 / 2.42 ( 281) hydrogen bonds : angle 4.74063 / 3.52 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1083.48 seconds wall clock time: 19 minutes 6.30 seconds (1146.30 seconds total)