Starting phenix.real_space_refine on Tue Aug 4 12:04:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9x_65792/08_2026/9w9x_65792.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9x_65792/08_2026/9w9x_65792.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/9w9x_65792/08_2026/9w9x_65792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9x_65792/08_2026/9w9x_65792.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9x_65792/08_2026/9w9x_65792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9x_65792/08_2026/9w9x_65792.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= 0.000 sd= 0.004 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 3 5.16 5 C 1413 2.51 5 N 366 2.21 5 O 405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2187 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 729 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "A" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 729 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 729 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 0.66, per 1000 atoms: 0.30 Number of scatterers: 2187 At special positions: 0 Unit cell: (76.26, 81.84, 31.62, 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 3 16.00 O 405 8.00 N 366 7.00 C 1413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.09 Conformation dependent library (CDL) restraints added in 49.0 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 534 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 55.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.578A pdb=" N MET C 13 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 16 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS C 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 removed outlier: 6.368A pdb=" N ALA C 25 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN C 27 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 30 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 29 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL A 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N HIS C 31 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ARG A 34 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE C 33 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.804A pdb=" N THR C 59 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU A 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU C 61 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE A 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU C 63 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.453A pdb=" N TYR C 69 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLU A 72 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL C 71 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 80 removed outlier: 6.949A pdb=" N SER C 77 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR A 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N LYS C 76 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N TRP B 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR C 78 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.427A pdb=" N ARG C 83 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 99 removed outlier: 6.359A pdb=" N GLU C 92 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE B 95 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 94 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA B 97 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 96 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ASP B 99 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 98 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 110 removed outlier: 7.006A pdb=" N ALA C 109 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG C 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE B 107 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR C 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA B 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA C 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.894A pdb=" N TYR C 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 123 removed outlier: 5.971A pdb=" N THR C 118 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA C 120 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR A 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 122 " --> pdb=" O THR A 123 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 147 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: 0.20 Time building geometry restraints manager: 0.13 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: 687 1.34 - 1.46: 450 1.46 - 1.57: 1095 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2238 Sorted by residual: bond pdb=" C VAL A 121 " pdb=" O VAL A 121 " ideal model delta sigma weight residual 1.237 1.229 0.009 1.08e-02 8.57e+03 6.37e-01 bond pdb=" C VAL C 121 " pdb=" O VAL C 121 " ideal model delta sigma weight residual 1.237 1.229 0.008 1.08e-02 8.57e+03 6.16e-01 bond pdb=" CA GLU B 66 " pdb=" C GLU B 66 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.00e-01 bond pdb=" C VAL B 121 " pdb=" O VAL B 121 " ideal model delta sigma weight residual 1.237 1.229 0.008 1.08e-02 8.57e+03 5.72e-01 bond pdb=" CA GLU A 66 " pdb=" C GLU A 66 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.71e-01 ... (remaining 2233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 2873 1.15 - 2.30: 124 2.30 - 3.46: 36 3.46 - 4.61: 6 4.61 - 5.76: 6 Bond angle restraints: 3045 Sorted by residual: angle pdb=" N ILE C 68 " pdb=" CA ILE C 68 " pdb=" C ILE C 68 " ideal model delta sigma weight residual 111.48 108.81 2.67 9.40e-01 1.13e+00 8.06e+00 angle pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" C ILE A 68 " ideal model delta sigma weight residual 111.48 108.84 2.64 9.40e-01 1.13e+00 7.88e+00 angle pdb=" N VAL C 122 " pdb=" CA VAL C 122 " pdb=" C VAL C 122 " ideal model delta sigma weight residual 108.11 112.01 -3.90 1.40e+00 5.10e-01 7.75e+00 angle pdb=" N VAL B 122 " pdb=" CA VAL B 122 " pdb=" C VAL B 122 " ideal model delta sigma weight residual 108.11 111.99 -3.88 1.40e+00 5.10e-01 7.67e+00 angle pdb=" N ILE B 68 " pdb=" CA ILE B 68 " pdb=" C ILE B 68 " ideal model delta sigma weight residual 111.48 108.88 2.60 9.40e-01 1.13e+00 7.63e+00 ... (remaining 3040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 1176 17.62 - 35.24: 105 35.24 - 52.86: 36 52.86 - 70.48: 9 70.48 - 88.09: 6 Dihedral angle restraints: 1332 sinusoidal: 513 harmonic: 819 Sorted by residual: dihedral pdb=" CB GLU B 72 " pdb=" CG GLU B 72 " pdb=" CD GLU B 72 " pdb=" OE1 GLU B 72 " ideal model delta sinusoidal sigma weight residual 0.00 -88.09 88.09 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU C 72 " pdb=" CG GLU C 72 " pdb=" CD GLU C 72 " pdb=" OE1 GLU C 72 " ideal model delta sinusoidal sigma weight residual 0.00 -88.05 88.05 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 72 " pdb=" CG GLU A 72 " pdb=" CD GLU A 72 " pdb=" OE1 GLU A 72 " ideal model delta sinusoidal sigma weight residual 0.00 -88.04 88.04 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 1329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 174 0.027 - 0.053: 110 0.053 - 0.079: 25 0.079 - 0.106: 29 0.106 - 0.132: 22 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA VAL C 121 " pdb=" N VAL C 121 " pdb=" C VAL C 121 " pdb=" CB VAL C 121 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA VAL B 121 " pdb=" N VAL B 121 " pdb=" C VAL B 121 " pdb=" CB VAL B 121 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 357 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 101 " 0.013 5.00e-02 4.00e+02 1.92e-02 5.92e-01 pdb=" N PRO C 102 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 101 " 0.013 5.00e-02 4.00e+02 1.92e-02 5.91e-01 pdb=" N PRO A 102 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 101 " 0.013 5.00e-02 4.00e+02 1.92e-02 5.91e-01 pdb=" N PRO B 102 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " 0.011 5.00e-02 4.00e+02 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 237 2.77 - 3.30: 1845 3.30 - 3.84: 3705 3.84 - 4.37: 4113 4.37 - 4.90: 7913 Nonbonded interactions: 17813 Sorted by model distance: nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.241 3.040 nonbonded pdb=" O SER C 85 " pdb=" OG SER C 85 " model vdw 2.241 3.040 nonbonded pdb=" O SER A 85 " pdb=" OG SER A 85 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP B 74 " pdb=" OH TYR B 105 " model vdw 2.342 3.040 nonbonded pdb=" OD2 ASP A 74 " pdb=" OH TYR A 105 " model vdw 2.343 3.040 ... (remaining 17808 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } 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: 0.900 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.890 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 0.014 2238 Z= 0.129 Angle : 0.630 5.758 3045 Z= 0.372 Chirality : 0.049 0.132 360 Planarity : 0.004 0.027 375 Dihedral : 16.715 88.095 798 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 83 TYR 0.013 0.001 TYR A 114 PHE 0.011 0.001 PHE A 33 TRP 0.002 0.000 TRP C 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 ( 2238) covalent geometry : angle 0.62956 / 0.37 ( 3045) hydrogen bonds : bond 0.14496 / 10.52 ( 49) hydrogen bonds : angle 8.76707 / 6.41 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: C 89 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7333 (tp30) REVERT: B 63 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 83 ARG cc_start: 0.8271 (mpt180) cc_final: 0.7987 (mpp-170) REVERT: B 88 HIS cc_start: 0.7313 (m-70) cc_final: 0.5171 (p90) REVERT: B 99 ASP cc_start: 0.7778 (t0) cc_final: 0.7488 (t70) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.7027 time to fit residues: 32.6728 Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.0070 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 88 HIS A 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.148677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122233 restraints weight = 2209.339| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.69 r_work: 0.3707 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2238 Z= 0.091 Angle : 0.521 4.699 3045 Z= 0.282 Chirality : 0.050 0.141 360 Planarity : 0.003 0.026 375 Dihedral : 5.005 17.322 300 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.25 % Allowed : 14.58 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.013 0.001 TYR C 114 PHE 0.016 0.001 PHE B 33 TRP 0.004 0.001 TRP C 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 2238) covalent geometry : angle 0.52124 / 0.28 ( 3045) hydrogen bonds : bond 0.02707 / 1.99 ( 49) hydrogen bonds : angle 6.20532 / 4.34 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.052 Fit side-chains REVERT: C 104 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7988 (mtm180) REVERT: A 104 ARG cc_start: 0.8321 (mtm180) cc_final: 0.8083 (mtm180) REVERT: B 74 ASP cc_start: 0.8767 (t0) cc_final: 0.8559 (t0) REVERT: B 83 ARG cc_start: 0.8161 (mpt180) cc_final: 0.7854 (mpp-170) REVERT: B 88 HIS cc_start: 0.7462 (m-70) cc_final: 0.5158 (p-80) REVERT: B 99 ASP cc_start: 0.7980 (t0) cc_final: 0.7705 (t70) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.8808 time to fit residues: 41.8491 Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.143756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116206 restraints weight = 2218.009| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.71 r_work: 0.3608 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2238 Z= 0.194 Angle : 0.633 5.298 3045 Z= 0.349 Chirality : 0.054 0.147 360 Planarity : 0.004 0.017 375 Dihedral : 5.698 18.279 300 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.92 % Allowed : 15.00 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.014 0.002 TYR C 114 PHE 0.019 0.002 PHE B 33 TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 ( 2238) covalent geometry : angle 0.63269 / 0.35 ( 3045) hydrogen bonds : bond 0.02843 / 2.08 ( 49) hydrogen bonds : angle 5.90062 / 4.09 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.054 Fit side-chains REVERT: C 35 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7315 (mttt) REVERT: B 83 ARG cc_start: 0.8205 (mpt180) cc_final: 0.7970 (mpp-170) REVERT: B 88 HIS cc_start: 0.7537 (m-70) cc_final: 0.5137 (p-80) REVERT: B 99 ASP cc_start: 0.8229 (t0) cc_final: 0.7994 (t70) REVERT: B 104 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7996 (mtm180) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 0.9680 time to fit residues: 50.8688 Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.145957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118662 restraints weight = 2149.748| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.69 r_work: 0.3638 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2238 Z= 0.141 Angle : 0.570 4.832 3045 Z= 0.317 Chirality : 0.052 0.144 360 Planarity : 0.003 0.024 375 Dihedral : 5.588 18.847 300 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.17 % Allowed : 14.58 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.014 0.002 TYR C 114 PHE 0.018 0.002 PHE B 33 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 2238) covalent geometry : angle 0.57031 / 0.32 ( 3045) hydrogen bonds : bond 0.02469 / 1.81 ( 49) hydrogen bonds : angle 5.70144 / 3.93 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.052 Fit side-chains REVERT: C 104 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8020 (mtt180) REVERT: A 76 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8070 (mtmt) REVERT: B 83 ARG cc_start: 0.8210 (mpt180) cc_final: 0.7972 (mpp-170) REVERT: B 88 HIS cc_start: 0.7554 (m-70) cc_final: 0.5159 (p-80) REVERT: B 99 ASP cc_start: 0.8065 (t0) cc_final: 0.7829 (t70) REVERT: B 104 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7888 (mtm180) outliers start: 10 outliers final: 2 residues processed: 54 average time/residue: 0.9181 time to fit residues: 50.0999 Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.145182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.117903 restraints weight = 2162.946| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.70 r_work: 0.3631 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2238 Z= 0.142 Angle : 0.569 5.183 3045 Z= 0.316 Chirality : 0.052 0.143 360 Planarity : 0.003 0.022 375 Dihedral : 5.614 19.044 300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.33 % Allowed : 15.00 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.014 0.002 TYR C 114 PHE 0.018 0.002 PHE B 33 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 2238) covalent geometry : angle 0.56940 / 0.32 ( 3045) hydrogen bonds : bond 0.02444 / 1.79 ( 49) hydrogen bonds : angle 5.62471 / 3.87 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: C 104 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8064 (mtt180) REVERT: A 76 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8019 (mtmt) REVERT: B 83 ARG cc_start: 0.8241 (mpt180) cc_final: 0.7967 (mpp-170) REVERT: B 88 HIS cc_start: 0.7579 (m-70) cc_final: 0.5110 (p-80) REVERT: B 99 ASP cc_start: 0.8062 (t0) cc_final: 0.7824 (t70) REVERT: B 104 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7868 (mtm180) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.9789 time to fit residues: 51.4541 Evaluate side-chains 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117117 restraints weight = 2125.319| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.69 r_work: 0.3625 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2238 Z= 0.168 Angle : 0.596 5.295 3045 Z= 0.331 Chirality : 0.053 0.144 360 Planarity : 0.003 0.022 375 Dihedral : 5.730 19.061 300 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.75 % Allowed : 14.17 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.014 0.002 TYR C 114 PHE 0.018 0.002 PHE B 33 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 2238) covalent geometry : angle 0.59587 / 0.33 ( 3045) hydrogen bonds : bond 0.02523 / 1.85 ( 49) hydrogen bonds : angle 5.64448 / 3.88 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.053 Fit side-chains REVERT: C 104 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8003 (mtt180) REVERT: A 76 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8011 (mtmt) REVERT: A 104 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7991 (mtm180) REVERT: B 35 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7408 (mttt) REVERT: B 83 ARG cc_start: 0.8250 (mpt180) cc_final: 0.7987 (mpp-170) REVERT: B 88 HIS cc_start: 0.7589 (m-70) cc_final: 0.5107 (p-80) REVERT: B 99 ASP cc_start: 0.8066 (t0) cc_final: 0.7833 (t70) REVERT: B 104 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7888 (mtm180) outliers start: 9 outliers final: 2 residues processed: 51 average time/residue: 0.9159 time to fit residues: 47.2377 Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 0.0770 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.144299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.116697 restraints weight = 2164.524| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.71 r_work: 0.3628 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2238 Z= 0.159 Angle : 0.582 5.381 3045 Z= 0.324 Chirality : 0.052 0.145 360 Planarity : 0.003 0.021 375 Dihedral : 5.743 19.238 300 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.33 % Allowed : 15.83 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.014 0.002 TYR C 114 PHE 0.018 0.002 PHE B 33 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 2238) covalent geometry : angle 0.58249 / 0.32 ( 3045) hydrogen bonds : bond 0.02474 / 1.82 ( 49) hydrogen bonds : angle 5.64038 / 3.87 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.051 Fit side-chains REVERT: C 35 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7530 (mttt) REVERT: C 104 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8034 (mtt180) REVERT: A 76 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.7999 (mtmt) REVERT: B 83 ARG cc_start: 0.8270 (mpt180) cc_final: 0.8013 (mpp-170) REVERT: B 88 HIS cc_start: 0.7568 (m-70) cc_final: 0.5103 (p-80) REVERT: B 99 ASP cc_start: 0.8059 (t0) cc_final: 0.7830 (t70) REVERT: B 104 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7861 (mtm180) outliers start: 8 outliers final: 2 residues processed: 50 average time/residue: 0.7263 time to fit residues: 36.6859 Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.141443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.113580 restraints weight = 2179.286| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.73 r_work: 0.3583 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2238 Z= 0.252 Angle : 0.681 6.128 3045 Z= 0.379 Chirality : 0.056 0.145 360 Planarity : 0.004 0.022 375 Dihedral : 6.031 18.980 300 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.33 % Allowed : 15.83 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 104 TYR 0.014 0.003 TYR C 114 PHE 0.020 0.002 PHE B 33 TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 ( 2238) covalent geometry : angle 0.68146 / 0.38 ( 3045) hydrogen bonds : bond 0.02835 / 2.09 ( 49) hydrogen bonds : angle 5.82888 / 4.00 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.050 Fit side-chains REVERT: C 35 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7569 (mttt) REVERT: C 104 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8197 (mtt180) REVERT: A 76 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.7985 (mtmt) REVERT: B 35 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7438 (mttt) REVERT: B 83 ARG cc_start: 0.8298 (mpt180) cc_final: 0.8061 (mpp-170) REVERT: B 88 HIS cc_start: 0.7525 (m-70) cc_final: 0.5133 (p-80) REVERT: B 104 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8341 (mtt180) outliers start: 8 outliers final: 2 residues processed: 51 average time/residue: 0.7135 time to fit residues: 36.8092 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.146330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.118956 restraints weight = 2189.986| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.73 r_work: 0.3670 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2238 Z= 0.111 Angle : 0.538 5.326 3045 Z= 0.299 Chirality : 0.051 0.145 360 Planarity : 0.003 0.025 375 Dihedral : 5.625 19.284 300 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.33 % Allowed : 16.25 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.014 0.002 TYR C 114 PHE 0.016 0.002 PHE B 33 TRP 0.001 0.000 TRP A 79 HIS 0.001 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 2238) covalent geometry : angle 0.53839 / 0.30 ( 3045) hydrogen bonds : bond 0.02255 / 1.66 ( 49) hydrogen bonds : angle 5.61042 / 3.83 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.050 Fit side-chains REVERT: C 35 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7491 (mttt) REVERT: C 104 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8132 (mtt180) REVERT: A 76 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.7952 (mtmt) REVERT: B 35 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7464 (mttt) REVERT: B 83 ARG cc_start: 0.8259 (mpt180) cc_final: 0.8002 (mpp-170) REVERT: B 88 HIS cc_start: 0.7497 (m-70) cc_final: 0.5090 (p-80) REVERT: B 99 ASP cc_start: 0.8204 (t0) cc_final: 0.7975 (t70) REVERT: B 104 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8235 (mtt180) outliers start: 8 outliers final: 2 residues processed: 51 average time/residue: 0.7412 time to fit residues: 38.2304 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.148243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.120160 restraints weight = 2160.888| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.76 r_work: 0.3660 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2238 Z= 0.112 Angle : 0.543 6.190 3045 Z= 0.299 Chirality : 0.050 0.145 360 Planarity : 0.003 0.026 375 Dihedral : 5.540 19.403 300 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.33 % Allowed : 16.25 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.014 0.002 TYR C 114 PHE 0.016 0.002 PHE B 33 TRP 0.001 0.000 TRP C 79 HIS 0.001 0.000 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 2238) covalent geometry : angle 0.54264 / 0.30 ( 3045) hydrogen bonds : bond 0.02291 / 1.68 ( 49) hydrogen bonds : angle 5.51441 / 3.78 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.103 Fit side-chains REVERT: C 35 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7489 (mttt) REVERT: C 104 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8207 (mtt180) REVERT: A 76 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.7978 (mtmt) REVERT: B 35 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7450 (mttt) REVERT: B 83 ARG cc_start: 0.8201 (mpt180) cc_final: 0.7913 (mpp-170) REVERT: B 88 HIS cc_start: 0.7506 (m-70) cc_final: 0.5113 (p-80) REVERT: B 99 ASP cc_start: 0.8215 (t0) cc_final: 0.7999 (t0) REVERT: B 104 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8247 (mtt180) outliers start: 8 outliers final: 2 residues processed: 52 average time/residue: 0.6224 time to fit residues: 32.7818 Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.146360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.117970 restraints weight = 2203.513| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.78 r_work: 0.3650 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2238 Z= 0.153 Angle : 0.596 7.249 3045 Z= 0.328 Chirality : 0.052 0.144 360 Planarity : 0.003 0.024 375 Dihedral : 5.737 19.518 300 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.50 % Allowed : 17.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.014 0.002 TYR C 114 PHE 0.018 0.002 PHE B 33 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 2238) covalent geometry : angle 0.59642 / 0.33 ( 3045) hydrogen bonds : bond 0.02431 / 1.78 ( 49) hydrogen bonds : angle 5.56063 / 3.81 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1197.88 seconds wall clock time: 21 minutes 3.06 seconds (1263.06 seconds total)