Starting phenix.real_space_refine on Tue Feb 3 12:58:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdk_61394/02_2026/9jdk_61394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdk_61394/02_2026/9jdk_61394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jdk_61394/02_2026/9jdk_61394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdk_61394/02_2026/9jdk_61394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jdk_61394/02_2026/9jdk_61394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdk_61394/02_2026/9jdk_61394.map" } resolution = 3.32 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= 0.003 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: 3 Type Number sf(0) Gaussians C 1662 2.51 5 N 456 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2664 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 0.79, per 1000 atoms: 0.30 Number of scatterers: 2664 At special positions: 0 Unit cell: (109.56, 86.32, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 546 8.00 N 456 7.00 C 1662 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: 0.21 Conformation dependent library (CDL) restraints added in 109.5 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.433A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 6.315A pdb=" N VAL A 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL E 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP A 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N THR E 54 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N THR A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 52 " --> pdb=" O ASP E 51 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR E 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C 54 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL E 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.517A pdb=" N GLN C 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASN E 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.429A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 82 removed outlier: 6.842A pdb=" N THR E 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 82 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N LYS E 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLN C 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL E 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N THR C 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.309A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 94 through 96 removed outlier: 6.731A pdb=" N VAL C 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.828A pdb=" N VAL B 52 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR F 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 54 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASP D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N THR F 54 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 66 removed outlier: 6.138A pdb=" N VAL D 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL F 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.390A pdb=" N ALA B 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.943A pdb=" N THR B 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL F 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU B 83 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA D 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN F 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N GLU F 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N VAL D 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.320A pdb=" N ILE D 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 94 through 96 removed outlier: 6.381A pdb=" N VAL B 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 99 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: 0.33 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 474 1.28 - 1.35: 408 1.35 - 1.41: 99 1.41 - 1.48: 441 1.48 - 1.54: 1254 Bond restraints: 2676 Sorted by residual: bond pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " ideal model delta sigma weight residual 1.534 1.505 0.029 2.33e-02 1.84e+03 1.54e+00 bond pdb=" CA GLN A 79 " pdb=" CB GLN A 79 " ideal model delta sigma weight residual 1.534 1.506 0.029 2.33e-02 1.84e+03 1.53e+00 bond pdb=" CA GLN E 79 " pdb=" CB GLN E 79 " ideal model delta sigma weight residual 1.534 1.506 0.028 2.33e-02 1.84e+03 1.49e+00 bond pdb=" CB VAL A 48 " pdb=" CG1 VAL A 48 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CG GLN C 79 " pdb=" CD GLN C 79 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.12e+00 ... (remaining 2671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 3453 1.47 - 2.94: 141 2.94 - 4.41: 18 4.41 - 5.87: 9 5.87 - 7.34: 3 Bond angle restraints: 3624 Sorted by residual: angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.87 117.38 4.49 1.64e+00 3.72e-01 7.48e+00 angle pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta sigma weight residual 121.87 117.39 4.48 1.64e+00 3.72e-01 7.45e+00 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 121.87 117.40 4.47 1.64e+00 3.72e-01 7.42e+00 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 121.80 117.28 4.52 1.71e+00 3.42e-01 7.00e+00 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 121.80 117.29 4.51 1.71e+00 3.42e-01 6.97e+00 ... (remaining 3619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.08: 1414 13.08 - 26.16: 117 26.16 - 39.24: 32 39.24 - 52.32: 9 52.32 - 65.41: 6 Dihedral angle restraints: 1578 sinusoidal: 540 harmonic: 1038 Sorted by residual: dihedral pdb=" CA GLU F 46 " pdb=" C GLU F 46 " pdb=" N GLY F 47 " pdb=" CA GLY F 47 " ideal model delta harmonic sigma weight residual 180.00 164.78 15.22 0 5.00e+00 4.00e-02 9.26e+00 dihedral pdb=" CA GLU D 46 " pdb=" C GLU D 46 " pdb=" N GLY D 47 " pdb=" CA GLY D 47 " ideal model delta harmonic sigma weight residual 180.00 164.80 15.20 0 5.00e+00 4.00e-02 9.25e+00 dihedral pdb=" CA GLU B 46 " pdb=" C GLU B 46 " pdb=" N GLY B 47 " pdb=" CA GLY B 47 " ideal model delta harmonic sigma weight residual 180.00 164.84 15.16 0 5.00e+00 4.00e-02 9.19e+00 ... (remaining 1575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 192 0.032 - 0.063: 170 0.063 - 0.095: 61 0.095 - 0.126: 48 0.126 - 0.158: 9 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 477 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.011 2.00e-02 2.50e+03 9.90e-03 1.47e+00 pdb=" CG HIS A 50 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.011 2.00e-02 2.50e+03 9.76e-03 1.43e+00 pdb=" CG HIS E 50 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " 0.011 2.00e-02 2.50e+03 9.64e-03 1.39e+00 pdb=" CG HIS C 50 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " 0.003 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 267 2.75 - 3.29: 2458 3.29 - 3.82: 4162 3.82 - 4.36: 4417 4.36 - 4.90: 9295 Nonbonded interactions: 20599 Sorted by model distance: nonbonded pdb=" CE LYS E 43 " pdb=" OE2 GLU F 57 " model vdw 2.212 3.440 nonbonded pdb=" CE LYS C 43 " pdb=" OE2 GLU D 57 " model vdw 2.212 3.440 nonbonded pdb=" CE LYS A 43 " pdb=" OE2 GLU B 57 " model vdw 2.212 3.440 nonbonded pdb=" CE LYS A 43 " pdb=" OE1 GLU B 57 " model vdw 2.439 3.440 nonbonded pdb=" CE LYS C 43 " pdb=" OE1 GLU D 57 " model vdw 2.439 3.440 ... (remaining 20594 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.008 0.035 2676 Z= 0.386 Angle : 0.756 7.343 3624 Z= 0.449 Chirality : 0.057 0.158 480 Planarity : 0.003 0.010 450 Dihedral : 12.046 65.405 918 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % 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: -4.18 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 39 PHE 0.017 0.003 PHE C 94 HIS 0.008 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00820 ( 2676) covalent geometry : angle 0.75552 ( 3624) hydrogen bonds : bond 0.20110 ( 33) hydrogen bonds : angle 8.79538 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6932 (mm110) REVERT: B 43 LYS cc_start: 0.8120 (mttt) cc_final: 0.7777 (mtpt) REVERT: B 97 LYS cc_start: 0.8190 (mttm) cc_final: 0.7934 (mtmt) REVERT: B 99 GLN cc_start: 0.7540 (mm110) cc_final: 0.7209 (mm-40) REVERT: C 99 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6600 (mm110) REVERT: D 43 LYS cc_start: 0.8325 (mttt) cc_final: 0.8035 (mtmt) REVERT: D 97 LYS cc_start: 0.8615 (mttm) cc_final: 0.8248 (mtmt) REVERT: D 99 GLN cc_start: 0.7921 (mm110) cc_final: 0.7667 (mm-40) REVERT: E 99 GLN cc_start: 0.6749 (mm-40) cc_final: 0.6336 (mm110) REVERT: F 43 LYS cc_start: 0.8082 (mttt) cc_final: 0.7738 (mtpt) REVERT: F 97 LYS cc_start: 0.8081 (mttm) cc_final: 0.7757 (mtmt) REVERT: F 99 GLN cc_start: 0.7556 (mm110) cc_final: 0.7156 (mm110) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0965 time to fit residues: 3.8936 Evaluate side-chains 34 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097257 restraints weight = 3138.854| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.65 r_work: 0.3383 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2676 Z= 0.186 Angle : 0.565 9.236 3624 Z= 0.306 Chirality : 0.053 0.157 480 Planarity : 0.002 0.009 450 Dihedral : 4.348 13.103 378 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.19 % Allowed : 8.51 % Favored : 88.30 % 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: -3.30 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.012 0.002 PHE E 94 HIS 0.007 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 2676) covalent geometry : angle 0.56479 ( 3624) hydrogen bonds : bond 0.02562 ( 33) hydrogen bonds : angle 6.45639 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8781 (mttm) cc_final: 0.8510 (mttt) REVERT: B 43 LYS cc_start: 0.8047 (mttt) cc_final: 0.7705 (mtpt) REVERT: B 97 LYS cc_start: 0.8220 (mttm) cc_final: 0.8017 (mtmt) REVERT: B 99 GLN cc_start: 0.7136 (mm110) cc_final: 0.6819 (mm-40) REVERT: C 99 GLN cc_start: 0.6921 (mm-40) cc_final: 0.6517 (mm110) REVERT: D 43 LYS cc_start: 0.8323 (mttt) cc_final: 0.8030 (mtmt) REVERT: D 97 LYS cc_start: 0.8661 (mttm) cc_final: 0.8235 (mtmt) REVERT: D 99 GLN cc_start: 0.7798 (mm110) cc_final: 0.7473 (mm-40) REVERT: E 43 LYS cc_start: 0.8734 (mttp) cc_final: 0.8362 (mttt) REVERT: E 99 GLN cc_start: 0.6595 (mm-40) cc_final: 0.6204 (mm-40) REVERT: F 43 LYS cc_start: 0.8072 (mttt) cc_final: 0.7801 (mtmt) REVERT: F 97 LYS cc_start: 0.8150 (mttm) cc_final: 0.7819 (mtmt) REVERT: F 99 GLN cc_start: 0.7145 (mm110) cc_final: 0.6697 (mm110) outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.0764 time to fit residues: 3.3597 Evaluate side-chains 41 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.0470 chunk 19 optimal weight: 8.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.124234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099953 restraints weight = 3121.240| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.60 r_work: 0.3425 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2676 Z= 0.129 Angle : 0.502 8.873 3624 Z= 0.268 Chirality : 0.051 0.147 480 Planarity : 0.002 0.007 450 Dihedral : 3.950 11.671 378 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.13 % Allowed : 9.93 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR F 39 PHE 0.009 0.002 PHE E 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2676) covalent geometry : angle 0.50194 ( 3624) hydrogen bonds : bond 0.01990 ( 33) hydrogen bonds : angle 5.97754 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8765 (mttm) cc_final: 0.8501 (mttt) REVERT: B 43 LYS cc_start: 0.8043 (mttt) cc_final: 0.7728 (mtmt) REVERT: B 99 GLN cc_start: 0.7070 (mm110) cc_final: 0.6744 (mm-40) REVERT: C 99 GLN cc_start: 0.6859 (mm-40) cc_final: 0.6464 (mm110) REVERT: D 43 LYS cc_start: 0.8307 (mttt) cc_final: 0.8016 (mtmt) REVERT: D 97 LYS cc_start: 0.8646 (mttm) cc_final: 0.8211 (mtmt) REVERT: D 99 GLN cc_start: 0.7752 (mm110) cc_final: 0.7344 (mm-40) REVERT: E 43 LYS cc_start: 0.8692 (mttp) cc_final: 0.8314 (mttt) REVERT: E 99 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6359 (mm110) REVERT: F 43 LYS cc_start: 0.8055 (mttt) cc_final: 0.7808 (mtmt) REVERT: F 97 LYS cc_start: 0.8147 (mttm) cc_final: 0.7818 (mtmt) REVERT: F 99 GLN cc_start: 0.7098 (mm110) cc_final: 0.6600 (mm110) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.0970 time to fit residues: 4.0091 Evaluate side-chains 38 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.123359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099132 restraints weight = 3149.423| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.56 r_work: 0.3407 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2676 Z= 0.163 Angle : 0.510 7.927 3624 Z= 0.277 Chirality : 0.051 0.149 480 Planarity : 0.002 0.008 450 Dihedral : 4.004 11.481 378 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.19 % Allowed : 9.93 % Favored : 86.88 % 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: -2.34 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.010 0.002 PHE E 94 HIS 0.007 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 2676) covalent geometry : angle 0.51025 ( 3624) hydrogen bonds : bond 0.01941 ( 33) hydrogen bonds : angle 5.78378 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8823 (mttm) cc_final: 0.8524 (mttt) REVERT: B 43 LYS cc_start: 0.7965 (mttt) cc_final: 0.7698 (mtmt) REVERT: B 99 GLN cc_start: 0.7131 (mm110) cc_final: 0.6780 (mm-40) REVERT: C 99 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6496 (mm110) REVERT: D 43 LYS cc_start: 0.8313 (mttt) cc_final: 0.8016 (mtmt) REVERT: D 97 LYS cc_start: 0.8629 (mttm) cc_final: 0.8211 (mtmt) REVERT: E 43 LYS cc_start: 0.8701 (mttp) cc_final: 0.8306 (mttt) REVERT: E 99 GLN cc_start: 0.6627 (mm-40) cc_final: 0.6348 (mm110) REVERT: F 43 LYS cc_start: 0.8010 (mttt) cc_final: 0.7742 (mtmt) REVERT: F 97 LYS cc_start: 0.8149 (mttm) cc_final: 0.7814 (mtmt) REVERT: F 99 GLN cc_start: 0.7070 (mm110) cc_final: 0.6632 (mm110) outliers start: 9 outliers final: 7 residues processed: 37 average time/residue: 0.0817 time to fit residues: 3.5243 Evaluate side-chains 40 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095707 restraints weight = 3193.539| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.55 r_work: 0.3320 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2676 Z= 0.288 Angle : 0.609 9.831 3624 Z= 0.334 Chirality : 0.055 0.156 480 Planarity : 0.002 0.011 450 Dihedral : 4.480 13.143 378 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.32 % Allowed : 8.87 % Favored : 85.82 % 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: -2.28 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.014 0.003 PHE E 94 HIS 0.009 0.005 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 2676) covalent geometry : angle 0.60942 ( 3624) hydrogen bonds : bond 0.02339 ( 33) hydrogen bonds : angle 5.77417 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.105 Fit side-chains REVERT: A 43 LYS cc_start: 0.8914 (mttm) cc_final: 0.8547 (mttt) REVERT: B 43 LYS cc_start: 0.7942 (mttt) cc_final: 0.7679 (mtmt) REVERT: B 99 GLN cc_start: 0.7153 (mm110) cc_final: 0.6944 (mm-40) REVERT: C 43 LYS cc_start: 0.8639 (mttm) cc_final: 0.8241 (mttt) REVERT: C 80 LYS cc_start: 0.8803 (tttt) cc_final: 0.7656 (ttmt) REVERT: C 99 GLN cc_start: 0.6909 (mm-40) cc_final: 0.6515 (mm-40) REVERT: D 38 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7793 (tt) REVERT: D 43 LYS cc_start: 0.8346 (mttt) cc_final: 0.8044 (mtmt) REVERT: D 97 LYS cc_start: 0.8695 (mttm) cc_final: 0.8269 (mtmt) REVERT: D 99 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: E 43 LYS cc_start: 0.8775 (mttp) cc_final: 0.8332 (mttt) REVERT: E 99 GLN cc_start: 0.6574 (mm-40) cc_final: 0.6320 (mm110) REVERT: F 43 LYS cc_start: 0.7943 (mttt) cc_final: 0.7644 (mtmt) REVERT: F 97 LYS cc_start: 0.8183 (mttm) cc_final: 0.7898 (mtmt) outliers start: 15 outliers final: 9 residues processed: 45 average time/residue: 0.0918 time to fit residues: 4.7636 Evaluate side-chains 47 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107062 restraints weight = 3159.792| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.61 r_work: 0.3444 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2676 Z= 0.104 Angle : 0.463 8.402 3624 Z= 0.247 Chirality : 0.051 0.145 480 Planarity : 0.001 0.008 450 Dihedral : 3.800 10.642 378 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.77 % Allowed : 12.41 % Favored : 85.82 % 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: -2.14 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 39 PHE 0.008 0.002 PHE E 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 2676) covalent geometry : angle 0.46335 ( 3624) hydrogen bonds : bond 0.01694 ( 33) hydrogen bonds : angle 5.67368 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8810 (mttm) cc_final: 0.8527 (mttt) REVERT: B 43 LYS cc_start: 0.7925 (mttt) cc_final: 0.7684 (mtmt) REVERT: B 99 GLN cc_start: 0.7104 (mm110) cc_final: 0.6678 (mm-40) REVERT: C 99 GLN cc_start: 0.6697 (mm-40) cc_final: 0.6323 (mm110) REVERT: D 43 LYS cc_start: 0.8340 (mttt) cc_final: 0.7949 (mptt) REVERT: E 43 LYS cc_start: 0.8637 (mttp) cc_final: 0.8273 (mttt) REVERT: E 99 GLN cc_start: 0.6478 (mm-40) cc_final: 0.6214 (mm110) REVERT: F 43 LYS cc_start: 0.7964 (mttt) cc_final: 0.7670 (mtmt) REVERT: F 97 LYS cc_start: 0.8124 (mttm) cc_final: 0.7785 (mtmt) REVERT: F 99 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7013 (mm-40) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.0916 time to fit residues: 3.7302 Evaluate side-chains 35 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 0.0770 chunk 3 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.132434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.110239 restraints weight = 3041.479| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.45 r_work: 0.3538 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2676 Z= 0.076 Angle : 0.429 7.739 3624 Z= 0.228 Chirality : 0.050 0.141 480 Planarity : 0.001 0.007 450 Dihedral : 3.482 10.183 378 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.84 % Allowed : 11.35 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR D 39 PHE 0.007 0.001 PHE E 94 HIS 0.005 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00159 ( 2676) covalent geometry : angle 0.42871 ( 3624) hydrogen bonds : bond 0.01529 ( 33) hydrogen bonds : angle 5.44149 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8805 (mttm) cc_final: 0.8550 (mttt) REVERT: B 43 LYS cc_start: 0.7976 (mttt) cc_final: 0.7725 (mtmt) REVERT: B 99 GLN cc_start: 0.7117 (mm110) cc_final: 0.6708 (mm-40) REVERT: C 99 GLN cc_start: 0.6816 (mm-40) cc_final: 0.6484 (mm110) REVERT: D 43 LYS cc_start: 0.8269 (mttt) cc_final: 0.7820 (mmtm) REVERT: E 43 LYS cc_start: 0.8660 (mttp) cc_final: 0.8331 (mttt) REVERT: E 99 GLN cc_start: 0.6526 (mm-40) cc_final: 0.6276 (mm-40) REVERT: F 43 LYS cc_start: 0.7994 (mttt) cc_final: 0.7700 (mtmt) REVERT: F 97 LYS cc_start: 0.8149 (mttm) cc_final: 0.7796 (mtmt) REVERT: F 99 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7030 (mm-40) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.0781 time to fit residues: 3.3057 Evaluate side-chains 36 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.105425 restraints weight = 3155.750| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.61 r_work: 0.3398 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2676 Z= 0.148 Angle : 0.481 7.765 3624 Z= 0.260 Chirality : 0.051 0.146 480 Planarity : 0.002 0.010 450 Dihedral : 3.744 10.582 378 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.19 % Allowed : 11.35 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.009 0.002 PHE E 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2676) covalent geometry : angle 0.48068 ( 3624) hydrogen bonds : bond 0.01739 ( 33) hydrogen bonds : angle 5.43708 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8849 (mttm) cc_final: 0.8524 (mttt) REVERT: B 43 LYS cc_start: 0.7910 (mttt) cc_final: 0.7656 (mtmt) REVERT: B 99 GLN cc_start: 0.7110 (mm110) cc_final: 0.6669 (mm-40) REVERT: C 99 GLN cc_start: 0.6814 (mm-40) cc_final: 0.6433 (mm110) REVERT: D 38 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7730 (tt) REVERT: D 43 LYS cc_start: 0.8300 (mttt) cc_final: 0.7907 (mptt) REVERT: E 43 LYS cc_start: 0.8682 (mttp) cc_final: 0.8281 (mttt) REVERT: E 99 GLN cc_start: 0.6615 (mm-40) cc_final: 0.6342 (mm110) REVERT: F 43 LYS cc_start: 0.7828 (mttt) cc_final: 0.7521 (mtmt) REVERT: F 97 LYS cc_start: 0.8128 (mttm) cc_final: 0.7786 (mtmt) REVERT: F 99 GLN cc_start: 0.7394 (mm-40) cc_final: 0.6944 (mm-40) outliers start: 9 outliers final: 8 residues processed: 37 average time/residue: 0.0729 time to fit residues: 3.1577 Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.121696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097453 restraints weight = 3194.367| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.61 r_work: 0.3353 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2676 Z= 0.269 Angle : 0.578 8.763 3624 Z= 0.318 Chirality : 0.054 0.154 480 Planarity : 0.002 0.010 450 Dihedral : 4.262 11.728 378 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.26 % Allowed : 11.35 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR D 39 PHE 0.013 0.003 PHE C 94 HIS 0.009 0.005 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 2676) covalent geometry : angle 0.57761 ( 3624) hydrogen bonds : bond 0.02123 ( 33) hydrogen bonds : angle 5.49286 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.122 Fit side-chains REVERT: A 43 LYS cc_start: 0.8905 (mttm) cc_final: 0.8513 (mttt) REVERT: B 43 LYS cc_start: 0.7965 (mttt) cc_final: 0.7722 (mtmt) REVERT: B 99 GLN cc_start: 0.7184 (mm110) cc_final: 0.6891 (mm-40) REVERT: C 43 LYS cc_start: 0.8593 (mttm) cc_final: 0.8186 (mttt) REVERT: C 99 GLN cc_start: 0.6855 (mm-40) cc_final: 0.6464 (mm-40) REVERT: D 38 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7758 (tt) REVERT: D 43 LYS cc_start: 0.8306 (mttt) cc_final: 0.7940 (mptt) REVERT: D 97 LYS cc_start: 0.8463 (mttm) cc_final: 0.8116 (mtmt) REVERT: E 43 LYS cc_start: 0.8753 (mttp) cc_final: 0.8316 (mttt) REVERT: E 99 GLN cc_start: 0.6656 (mm-40) cc_final: 0.6392 (mm110) REVERT: F 43 LYS cc_start: 0.7864 (mttt) cc_final: 0.7555 (mtmt) REVERT: F 97 LYS cc_start: 0.8180 (mttm) cc_final: 0.7912 (mtmt) outliers start: 12 outliers final: 9 residues processed: 42 average time/residue: 0.0990 time to fit residues: 4.7905 Evaluate side-chains 46 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.127922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105157 restraints weight = 3200.727| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.60 r_work: 0.3435 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2676 Z= 0.162 Angle : 0.501 8.467 3624 Z= 0.271 Chirality : 0.052 0.150 480 Planarity : 0.002 0.009 450 Dihedral : 3.970 10.766 378 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.84 % Allowed : 12.41 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.010 0.002 PHE E 94 HIS 0.007 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 2676) covalent geometry : angle 0.50113 ( 3624) hydrogen bonds : bond 0.01851 ( 33) hydrogen bonds : angle 5.52016 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8877 (mttm) cc_final: 0.8548 (mttt) REVERT: B 43 LYS cc_start: 0.7997 (mttt) cc_final: 0.7752 (mtmt) REVERT: B 99 GLN cc_start: 0.7212 (mm110) cc_final: 0.6922 (mm-40) REVERT: C 99 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6511 (mm-40) REVERT: D 38 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7793 (tt) REVERT: D 43 LYS cc_start: 0.8285 (mttt) cc_final: 0.7916 (mptt) REVERT: E 43 LYS cc_start: 0.8757 (mttp) cc_final: 0.8377 (mttt) REVERT: E 99 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6411 (mm110) REVERT: F 43 LYS cc_start: 0.7926 (mttt) cc_final: 0.7629 (mtmt) REVERT: F 97 LYS cc_start: 0.8191 (mttm) cc_final: 0.7891 (mtmt) outliers start: 8 outliers final: 6 residues processed: 36 average time/residue: 0.0908 time to fit residues: 3.8248 Evaluate side-chains 39 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102134 restraints weight = 3191.204| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.62 r_work: 0.3358 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2676 Z= 0.206 Angle : 0.528 8.432 3624 Z= 0.289 Chirality : 0.052 0.152 480 Planarity : 0.002 0.009 450 Dihedral : 4.095 11.309 378 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.55 % Allowed : 11.70 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 39 PHE 0.011 0.002 PHE E 94 HIS 0.008 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 2676) covalent geometry : angle 0.52837 ( 3624) hydrogen bonds : bond 0.01972 ( 33) hydrogen bonds : angle 5.50687 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 796.12 seconds wall clock time: 14 minutes 23.21 seconds (863.21 seconds total)