Starting phenix.real_space_refine on Fri Aug 22 17:15:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dql_27656/08_2025/8dql_27656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dql_27656/08_2025/8dql_27656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dql_27656/08_2025/8dql_27656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dql_27656/08_2025/8dql_27656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dql_27656/08_2025/8dql_27656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dql_27656/08_2025/8dql_27656.map" } resolution = 3.0 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 9 5.16 5 C 4188 2.51 5 N 1026 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6402 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2134 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Restraints were copied for chains: A, B Time building chain proxies: 1.57, per 1000 atoms: 0.25 Number of scatterers: 6402 At special positions: 0 Unit cell: (95.7, 90.2, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 1179 8.00 N 1026 7.00 C 4188 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: 0.51 Conformation dependent library (CDL) restraints added in 317.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 45.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'C' and resid 15 through 34 removed outlier: 3.574A pdb=" N LEU C 19 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.510A pdb=" N LEU C 40 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 182 removed outlier: 3.732A pdb=" N ILE C 164 " --> pdb=" O TYR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 188 through 211 removed outlier: 4.180A pdb=" N ILE C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 193 " --> pdb=" O TYR C 189 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 4.122A pdb=" N ILE C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 268 removed outlier: 3.876A pdb=" N TYR C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 34 removed outlier: 3.574A pdb=" N LEU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.509A pdb=" N LEU A 40 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.732A pdb=" N ILE A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 188 through 211 removed outlier: 4.180A pdb=" N ILE A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 removed outlier: 4.122A pdb=" N ILE A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 268 removed outlier: 3.876A pdb=" N TYR A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 34 removed outlier: 3.574A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.509A pdb=" N LEU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.732A pdb=" N ILE B 164 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 188 through 211 removed outlier: 4.179A pdb=" N ILE B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 193 " --> pdb=" O TYR B 189 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 4.122A pdb=" N ILE B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 removed outlier: 3.876A pdb=" N TYR B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 49 removed outlier: 6.740A pdb=" N LYS C 65 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE C 47 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP C 63 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 49 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 61 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 121 removed outlier: 3.674A pdb=" N ALA C 135 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 99 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN C 133 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE C 101 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER C 131 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 136 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 49 removed outlier: 6.740A pdb=" N LYS A 65 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 47 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP A 63 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 49 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 61 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 121 removed outlier: 3.675A pdb=" N ALA A 135 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 99 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN A 133 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 101 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 131 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 136 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 49 removed outlier: 6.740A pdb=" N LYS B 65 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 47 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 63 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 49 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 61 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 111 through 121 removed outlier: 3.675A pdb=" N ALA B 135 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 99 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 133 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 101 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER B 131 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 136 " --> pdb=" O GLU B 147 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 891 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: 1.04 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2010 1.34 - 1.46: 928 1.46 - 1.57: 3569 1.57 - 1.69: 0 1.69 - 1.80: 15 Bond restraints: 6522 Sorted by residual: bond pdb=" CA ASN B 109 " pdb=" CB ASN B 109 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.04e-01 bond pdb=" CA ASN C 109 " pdb=" CB ASN C 109 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.55e-01 bond pdb=" CA ASN A 109 " pdb=" CB ASN A 109 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.34e-01 bond pdb=" CB ASP C 226 " pdb=" CG ASP C 226 " ideal model delta sigma weight residual 1.516 1.500 0.016 2.50e-02 1.60e+03 4.18e-01 bond pdb=" N ASN B 109 " pdb=" CA ASN B 109 " ideal model delta sigma weight residual 1.457 1.466 -0.008 1.29e-02 6.01e+03 3.98e-01 ... (remaining 6517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 8573 1.18 - 2.37: 168 2.37 - 3.55: 40 3.55 - 4.74: 15 4.74 - 5.92: 6 Bond angle restraints: 8802 Sorted by residual: angle pdb=" C LYS A 108 " pdb=" N ASN A 109 " pdb=" CA ASN A 109 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" C LYS C 108 " pdb=" N ASN C 109 " pdb=" CA ASN C 109 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.55e+00 angle pdb=" C LYS B 108 " pdb=" N ASN B 109 " pdb=" CA ASN B 109 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.50e+00 angle pdb=" CA ASN A 109 " pdb=" CB ASN A 109 " pdb=" CG ASN A 109 " ideal model delta sigma weight residual 112.60 114.50 -1.90 1.00e+00 1.00e+00 3.60e+00 angle pdb=" CA ASN B 109 " pdb=" CB ASN B 109 " pdb=" CG ASN B 109 " ideal model delta sigma weight residual 112.60 114.50 -1.90 1.00e+00 1.00e+00 3.60e+00 ... (remaining 8797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 3472 17.76 - 35.52: 407 35.52 - 53.28: 72 53.28 - 71.04: 9 71.04 - 88.79: 3 Dihedral angle restraints: 3963 sinusoidal: 1653 harmonic: 2310 Sorted by residual: dihedral pdb=" CA ASP A 63 " pdb=" CB ASP A 63 " pdb=" CG ASP A 63 " pdb=" OD1 ASP A 63 " ideal model delta sinusoidal sigma weight residual -30.00 -87.47 57.47 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP B 63 " pdb=" CB ASP B 63 " pdb=" CG ASP B 63 " pdb=" OD1 ASP B 63 " ideal model delta sinusoidal sigma weight residual -30.00 -87.39 57.39 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP C 63 " pdb=" CB ASP C 63 " pdb=" CG ASP C 63 " pdb=" OD1 ASP C 63 " ideal model delta sinusoidal sigma weight residual -30.00 -87.36 57.36 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 687 0.029 - 0.057: 208 0.057 - 0.086: 68 0.086 - 0.115: 36 0.115 - 0.144: 15 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA ASN A 109 " pdb=" N ASN A 109 " pdb=" C ASN A 109 " pdb=" CB ASN A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ASN C 109 " pdb=" N ASN C 109 " pdb=" C ASN C 109 " pdb=" CB ASN C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ASN B 109 " pdb=" N ASN B 109 " pdb=" C ASN B 109 " pdb=" CB ASN B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1011 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 108 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C LYS A 108 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS A 108 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN A 109 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 108 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C LYS B 108 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS B 108 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN B 109 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 108 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C LYS C 108 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS C 108 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 109 " 0.006 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1923 2.83 - 3.35: 5721 3.35 - 3.86: 9828 3.86 - 4.38: 10992 4.38 - 4.90: 19852 Nonbonded interactions: 48316 Sorted by model distance: nonbonded pdb=" O VAL C 45 " pdb=" OG1 THR C 155 " model vdw 2.309 3.040 nonbonded pdb=" O VAL A 45 " pdb=" OG1 THR A 155 " model vdw 2.309 3.040 nonbonded pdb=" O VAL B 45 " pdb=" OG1 THR B 155 " model vdw 2.309 3.040 nonbonded pdb=" NZ LYS A 104 " pdb=" OE1 GLN A 117 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS C 104 " pdb=" OE1 GLN C 117 " model vdw 2.341 3.120 ... (remaining 48311 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: 0.02 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: 2.860 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: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.540 Find NCS groups from input model: 0.060 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:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.020 6522 Z= 0.103 Angle : 0.473 5.921 8802 Z= 0.242 Chirality : 0.038 0.144 1014 Planarity : 0.002 0.012 1098 Dihedral : 14.893 88.795 2457 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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 aren not related in a simple way. whole: 2.01 (0.31), residues: 753 helix: 3.77 (0.26), residues: 309 sheet: 2.62 (0.64), residues: 63 loop : -1.12 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.004 0.001 TYR A 80 PHE 0.013 0.001 PHE B 2 TRP 0.001 0.000 TRP C 8 HIS 0.002 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6522) covalent geometry : angle 0.47275 ( 8802) hydrogen bonds : bond 0.16690 ( 315) hydrogen bonds : angle 5.99909 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.290 Fit side-chains REVERT: C 206 LYS cc_start: 0.8447 (tttm) cc_final: 0.8231 (ttpt) REVERT: A 224 ILE cc_start: 0.7981 (mt) cc_final: 0.7724 (mt) REVERT: B 206 LYS cc_start: 0.8534 (tttm) cc_final: 0.8332 (ttpp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.5771 time to fit residues: 54.0905 Evaluate side-chains 73 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103562 restraints weight = 9491.728| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.31 r_work: 0.3123 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6522 Z= 0.134 Angle : 0.562 7.879 8802 Z= 0.292 Chirality : 0.040 0.153 1014 Planarity : 0.003 0.035 1098 Dihedral : 3.513 15.436 843 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.92 % Allowed : 7.68 % Favored : 90.40 % 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 aren not related in a simple way. whole: 2.14 (0.32), residues: 753 helix: 3.98 (0.26), residues: 309 sheet: 2.93 (0.69), residues: 63 loop : -1.19 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 141 TYR 0.007 0.001 TYR B 76 PHE 0.022 0.001 PHE C 178 TRP 0.002 0.000 TRP A 8 HIS 0.003 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6522) covalent geometry : angle 0.56239 ( 8802) hydrogen bonds : bond 0.04883 ( 315) hydrogen bonds : angle 3.93785 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.267 Fit side-chains REVERT: C 8 TRP cc_start: 0.8225 (m100) cc_final: 0.7935 (m100) REVERT: C 21 LYS cc_start: 0.8426 (mttp) cc_final: 0.8137 (mttm) REVERT: C 206 LYS cc_start: 0.8918 (tttm) cc_final: 0.8566 (ttpt) REVERT: A 224 ILE cc_start: 0.8217 (mt) cc_final: 0.7935 (mt) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.5177 time to fit residues: 48.0540 Evaluate side-chains 73 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 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 = 0.3683 r_free = 0.3683 target = 0.132513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102272 restraints weight = 9430.976| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.31 r_work: 0.3139 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6522 Z= 0.132 Angle : 0.539 7.848 8802 Z= 0.279 Chirality : 0.040 0.152 1014 Planarity : 0.003 0.038 1098 Dihedral : 3.500 15.034 843 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.88 % Allowed : 9.88 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.31), residues: 753 helix: 3.95 (0.26), residues: 309 sheet: 2.96 (0.67), residues: 63 loop : -1.31 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 141 TYR 0.007 0.001 TYR B 76 PHE 0.017 0.001 PHE C 178 TRP 0.002 0.000 TRP A 8 HIS 0.002 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6522) covalent geometry : angle 0.53861 ( 8802) hydrogen bonds : bond 0.04783 ( 315) hydrogen bonds : angle 3.74293 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.271 Fit side-chains REVERT: C 8 TRP cc_start: 0.8256 (m100) cc_final: 0.7989 (m100) REVERT: C 21 LYS cc_start: 0.8476 (mttp) cc_final: 0.8204 (mttm) REVERT: C 206 LYS cc_start: 0.8914 (tttm) cc_final: 0.8591 (ttpt) REVERT: A 224 ILE cc_start: 0.8324 (mt) cc_final: 0.8047 (mt) REVERT: B 28 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: B 70 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7776 (tm-30) outliers start: 21 outliers final: 10 residues processed: 84 average time/residue: 0.4158 time to fit residues: 37.1684 Evaluate side-chains 78 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 38 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103417 restraints weight = 9492.296| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.36 r_work: 0.3141 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6522 Z= 0.117 Angle : 0.527 8.417 8802 Z= 0.274 Chirality : 0.039 0.146 1014 Planarity : 0.003 0.038 1098 Dihedral : 3.371 16.053 843 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.33 % Allowed : 10.56 % Favored : 87.11 % 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 aren not related in a simple way. whole: 2.00 (0.31), residues: 753 helix: 3.96 (0.26), residues: 309 sheet: 3.03 (0.66), residues: 63 loop : -1.40 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 141 TYR 0.006 0.001 TYR A 35 PHE 0.017 0.001 PHE C 178 TRP 0.003 0.001 TRP A 8 HIS 0.002 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6522) covalent geometry : angle 0.52681 ( 8802) hydrogen bonds : bond 0.04351 ( 315) hydrogen bonds : angle 3.58778 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.217 Fit side-chains REVERT: C 8 TRP cc_start: 0.8247 (m100) cc_final: 0.8000 (m100) REVERT: C 21 LYS cc_start: 0.8450 (mttp) cc_final: 0.8152 (mttm) REVERT: C 206 LYS cc_start: 0.8913 (tttm) cc_final: 0.8576 (ttpt) REVERT: A 224 ILE cc_start: 0.8197 (mt) cc_final: 0.7951 (mt) REVERT: B 28 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7468 (tm-30) outliers start: 17 outliers final: 6 residues processed: 84 average time/residue: 0.4502 time to fit residues: 40.0613 Evaluate side-chains 76 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 241 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 51 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108339 restraints weight = 9410.520| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.33 r_work: 0.3208 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6522 Z= 0.103 Angle : 0.491 8.468 8802 Z= 0.256 Chirality : 0.039 0.142 1014 Planarity : 0.003 0.038 1098 Dihedral : 3.260 15.138 843 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.61 % Allowed : 11.66 % Favored : 85.73 % 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 aren not related in a simple way. whole: 2.01 (0.31), residues: 753 helix: 3.95 (0.26), residues: 309 sheet: 3.02 (0.66), residues: 63 loop : -1.38 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.006 0.001 TYR A 35 PHE 0.018 0.001 PHE A 178 TRP 0.004 0.001 TRP A 8 HIS 0.001 0.000 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6522) covalent geometry : angle 0.49119 ( 8802) hydrogen bonds : bond 0.03993 ( 315) hydrogen bonds : angle 3.48157 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.202 Fit side-chains REVERT: C 8 TRP cc_start: 0.8242 (m100) cc_final: 0.8014 (m100) REVERT: C 70 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: C 206 LYS cc_start: 0.8918 (tttm) cc_final: 0.8575 (ttpt) REVERT: A 224 ILE cc_start: 0.8167 (mt) cc_final: 0.7952 (mt) outliers start: 19 outliers final: 10 residues processed: 88 average time/residue: 0.4522 time to fit residues: 42.0244 Evaluate side-chains 77 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099729 restraints weight = 9635.403| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.46 r_work: 0.3053 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6522 Z= 0.170 Angle : 0.569 6.516 8802 Z= 0.297 Chirality : 0.041 0.153 1014 Planarity : 0.003 0.044 1098 Dihedral : 3.588 15.039 843 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.43 % Allowed : 12.35 % Favored : 84.22 % 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 aren not related in a simple way. whole: 1.78 (0.31), residues: 753 helix: 3.74 (0.26), residues: 309 sheet: 3.05 (0.68), residues: 63 loop : -1.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 141 TYR 0.009 0.001 TYR B 76 PHE 0.015 0.002 PHE A 178 TRP 0.002 0.000 TRP B 8 HIS 0.003 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6522) covalent geometry : angle 0.56926 ( 8802) hydrogen bonds : bond 0.05470 ( 315) hydrogen bonds : angle 3.77665 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.262 Fit side-chains REVERT: C 70 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: C 206 LYS cc_start: 0.8916 (tttm) cc_final: 0.8528 (ttpt) REVERT: A 28 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: A 70 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: A 189 TYR cc_start: 0.8005 (m-10) cc_final: 0.7747 (m-10) REVERT: A 224 ILE cc_start: 0.8411 (mt) cc_final: 0.8127 (mt) REVERT: B 28 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7367 (tm-30) outliers start: 25 outliers final: 12 residues processed: 94 average time/residue: 0.4456 time to fit residues: 44.1754 Evaluate side-chains 81 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104092 restraints weight = 9220.981| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.25 r_work: 0.3145 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6522 Z= 0.144 Angle : 0.577 10.226 8802 Z= 0.297 Chirality : 0.040 0.171 1014 Planarity : 0.003 0.028 1098 Dihedral : 3.522 16.700 843 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.43 % Allowed : 13.44 % Favored : 83.13 % 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 aren not related in a simple way. whole: 1.75 (0.31), residues: 753 helix: 3.73 (0.26), residues: 309 sheet: 3.06 (0.68), residues: 63 loop : -1.56 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.008 0.001 TYR A 35 PHE 0.015 0.001 PHE A 178 TRP 0.004 0.001 TRP A 8 HIS 0.003 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6522) covalent geometry : angle 0.57735 ( 8802) hydrogen bonds : bond 0.04942 ( 315) hydrogen bonds : angle 3.72049 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.308 Fit side-chains REVERT: C 21 LYS cc_start: 0.8594 (mttm) cc_final: 0.8297 (mmmt) REVERT: C 206 LYS cc_start: 0.8918 (tttm) cc_final: 0.8578 (ttpt) REVERT: A 28 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: A 70 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: A 224 ILE cc_start: 0.8388 (mt) cc_final: 0.8115 (mt) REVERT: B 8 TRP cc_start: 0.8315 (m100) cc_final: 0.8033 (m100) REVERT: B 28 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7217 (tm-30) outliers start: 25 outliers final: 14 residues processed: 86 average time/residue: 0.4847 time to fit residues: 43.9931 Evaluate side-chains 85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 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 = 0.3653 r_free = 0.3653 target = 0.129890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099388 restraints weight = 9512.499| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.38 r_work: 0.3051 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6522 Z= 0.180 Angle : 0.613 7.189 8802 Z= 0.316 Chirality : 0.042 0.204 1014 Planarity : 0.004 0.053 1098 Dihedral : 3.719 17.508 843 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.16 % Allowed : 14.27 % Favored : 82.58 % 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 aren not related in a simple way. whole: 1.54 (0.31), residues: 753 helix: 3.55 (0.26), residues: 309 sheet: 3.00 (0.69), residues: 63 loop : -1.68 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 141 TYR 0.009 0.001 TYR A 115 PHE 0.027 0.002 PHE C 178 TRP 0.003 0.001 TRP A 8 HIS 0.002 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6522) covalent geometry : angle 0.61323 ( 8802) hydrogen bonds : bond 0.05639 ( 315) hydrogen bonds : angle 3.85891 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.191 Fit side-chains REVERT: C 21 LYS cc_start: 0.8686 (mttm) cc_final: 0.8287 (mmmt) REVERT: C 206 LYS cc_start: 0.8905 (tttm) cc_final: 0.8528 (ttpt) REVERT: C 226 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8160 (t0) REVERT: A 28 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 70 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: A 224 ILE cc_start: 0.8445 (mt) cc_final: 0.8191 (mt) REVERT: B 8 TRP cc_start: 0.8360 (m100) cc_final: 0.8066 (m100) REVERT: B 28 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7350 (tm-30) outliers start: 23 outliers final: 15 residues processed: 85 average time/residue: 0.4570 time to fit residues: 40.9366 Evaluate side-chains 88 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 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 = 0.3701 r_free = 0.3701 target = 0.133633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104370 restraints weight = 9385.280| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.32 r_work: 0.3139 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6522 Z= 0.147 Angle : 0.575 6.825 8802 Z= 0.295 Chirality : 0.040 0.162 1014 Planarity : 0.003 0.030 1098 Dihedral : 3.616 17.161 843 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.88 % Allowed : 14.81 % Favored : 82.30 % 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 aren not related in a simple way. whole: 1.62 (0.31), residues: 753 helix: 3.64 (0.27), residues: 309 sheet: 2.96 (0.69), residues: 63 loop : -1.64 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 102 TYR 0.008 0.001 TYR A 35 PHE 0.026 0.001 PHE C 178 TRP 0.003 0.001 TRP C 8 HIS 0.003 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6522) covalent geometry : angle 0.57461 ( 8802) hydrogen bonds : bond 0.04990 ( 315) hydrogen bonds : angle 3.75973 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.259 Fit side-chains REVERT: C 206 LYS cc_start: 0.8899 (tttm) cc_final: 0.8569 (ttpt) REVERT: C 226 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8111 (t0) REVERT: A 28 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: A 70 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: A 224 ILE cc_start: 0.8404 (mt) cc_final: 0.8133 (mt) REVERT: B 8 TRP cc_start: 0.8364 (m100) cc_final: 0.8063 (m100) REVERT: B 28 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7216 (tm-30) outliers start: 21 outliers final: 14 residues processed: 81 average time/residue: 0.4687 time to fit residues: 40.2343 Evaluate side-chains 85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 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 = 0.3717 r_free = 0.3717 target = 0.134846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105032 restraints weight = 9215.099| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.26 r_work: 0.3163 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6522 Z= 0.127 Angle : 0.576 7.409 8802 Z= 0.291 Chirality : 0.040 0.181 1014 Planarity : 0.003 0.030 1098 Dihedral : 3.543 17.286 843 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.33 % Allowed : 15.50 % Favored : 82.17 % 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 aren not related in a simple way. whole: 1.67 (0.32), residues: 753 helix: 3.70 (0.27), residues: 309 sheet: 2.92 (0.68), residues: 63 loop : -1.61 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 102 TYR 0.008 0.001 TYR A 115 PHE 0.026 0.001 PHE C 178 TRP 0.004 0.001 TRP C 8 HIS 0.002 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6522) covalent geometry : angle 0.57590 ( 8802) hydrogen bonds : bond 0.04577 ( 315) hydrogen bonds : angle 3.68076 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.186 Fit side-chains REVERT: C 206 LYS cc_start: 0.8880 (tttm) cc_final: 0.8551 (ttpt) REVERT: C 226 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8185 (t0) REVERT: A 28 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: A 70 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: A 224 ILE cc_start: 0.8300 (mt) cc_final: 0.8048 (mt) REVERT: B 8 TRP cc_start: 0.8303 (m100) cc_final: 0.8016 (m100) REVERT: B 28 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7199 (tm-30) outliers start: 17 outliers final: 10 residues processed: 80 average time/residue: 0.4300 time to fit residues: 36.5551 Evaluate side-chains 79 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105032 restraints weight = 9235.903| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.25 r_work: 0.3157 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6522 Z= 0.133 Angle : 0.585 11.144 8802 Z= 0.293 Chirality : 0.040 0.168 1014 Planarity : 0.003 0.031 1098 Dihedral : 3.545 17.202 843 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.06 % Allowed : 16.05 % Favored : 81.89 % 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 aren not related in a simple way. whole: 1.66 (0.32), residues: 753 helix: 3.70 (0.27), residues: 309 sheet: 2.90 (0.68), residues: 63 loop : -1.62 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 102 TYR 0.009 0.001 TYR A 35 PHE 0.025 0.001 PHE C 178 TRP 0.004 0.001 TRP C 8 HIS 0.002 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6522) covalent geometry : angle 0.58479 ( 8802) hydrogen bonds : bond 0.04679 ( 315) hydrogen bonds : angle 3.68207 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.24 seconds wall clock time: 36 minutes 44.81 seconds (2204.81 seconds total)