Starting phenix.real_space_refine on Tue Feb 11 17:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dql_27656/02_2025/8dql_27656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dql_27656/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dql_27656/02_2025/8dql_27656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dql_27656/02_2025/8dql_27656.map" model { file = "/net/cci-nas-00/data/ceres_data/8dql_27656/02_2025/8dql_27656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dql_27656/02_2025/8dql_27656.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6402 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B Time building chain proxies: 4.01, per 1000 atoms: 0.63 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: 1.59 Conformation dependent library (CDL) restraints added in 774.6 milliseconds 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: 0.50 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: 1.53 Time building geometry restraints manager: 1.82 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 1.240 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:15.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- 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= 0.137 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.001 0.000 TRP C 8 HIS 0.002 0.001 HIS C 158 PHE 0.013 0.001 PHE B 2 TYR 0.004 0.001 TYR A 80 ARG 0.003 0.000 ARG A 187 *********************** 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 : 0.727 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: 1.1106 time to fit residues: 104.5757 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 : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101241 restraints weight = 9505.320| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.44 r_work: 0.3081 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6522 Z= 0.243 Angle : 0.596 8.174 8802 Z= 0.309 Chirality : 0.041 0.158 1014 Planarity : 0.004 0.040 1098 Dihedral : 3.648 16.824 843 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.06 % Allowed : 7.96 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.31), residues: 753 helix: 3.90 (0.26), residues: 309 sheet: 2.86 (0.68), residues: 63 loop : -1.27 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 8 HIS 0.003 0.001 HIS C 158 PHE 0.021 0.002 PHE C 178 TYR 0.009 0.001 TYR B 76 ARG 0.005 0.000 ARG A 141 *********************** 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 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.794 Fit side-chains REVERT: C 8 TRP cc_start: 0.8273 (m100) cc_final: 0.8024 (m100) REVERT: C 206 LYS cc_start: 0.8840 (tttm) cc_final: 0.8468 (ttpt) REVERT: A 224 ILE cc_start: 0.8369 (mt) cc_final: 0.8102 (mt) outliers start: 15 outliers final: 8 residues processed: 86 average time/residue: 1.1317 time to fit residues: 103.0993 Evaluate side-chains 74 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.131501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101240 restraints weight = 9401.538| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.28 r_work: 0.3120 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6522 Z= 0.213 Angle : 0.556 7.873 8802 Z= 0.289 Chirality : 0.040 0.153 1014 Planarity : 0.003 0.037 1098 Dihedral : 3.603 15.396 843 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.31), residues: 753 helix: 3.85 (0.26), residues: 309 sheet: 2.94 (0.66), residues: 63 loop : -1.41 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 8 HIS 0.003 0.001 HIS C 158 PHE 0.017 0.001 PHE C 178 TYR 0.008 0.001 TYR A 35 ARG 0.006 0.001 ARG A 141 *********************** 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 93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.719 Fit side-chains REVERT: C 8 TRP cc_start: 0.8291 (m100) cc_final: 0.8057 (m100) REVERT: C 206 LYS cc_start: 0.8900 (tttm) cc_final: 0.8578 (ttpt) REVERT: A 224 ILE cc_start: 0.8367 (mt) cc_final: 0.8092 (mt) REVERT: B 28 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: B 70 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7668 (tm-30) outliers start: 21 outliers final: 10 residues processed: 82 average time/residue: 0.9869 time to fit residues: 86.3662 Evaluate side-chains 77 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL 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 184 SER 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 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.130536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099542 restraints weight = 9647.993| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.48 r_work: 0.3054 rms_B_bonded: 3.08 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: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6522 Z= 0.243 Angle : 0.586 8.623 8802 Z= 0.306 Chirality : 0.041 0.160 1014 Planarity : 0.004 0.040 1098 Dihedral : 3.644 15.702 843 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.74 % Allowed : 11.25 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.31), residues: 753 helix: 3.74 (0.26), residues: 309 sheet: 2.89 (0.67), residues: 63 loop : -1.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 8 HIS 0.003 0.001 HIS C 158 PHE 0.017 0.002 PHE A 178 TYR 0.010 0.001 TYR A 35 ARG 0.007 0.001 ARG B 141 *********************** 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 95 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.764 Fit side-chains REVERT: C 206 LYS cc_start: 0.8869 (tttm) cc_final: 0.8492 (ttpt) REVERT: A 224 ILE cc_start: 0.8397 (mt) cc_final: 0.8104 (mt) REVERT: B 28 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7468 (tm-30) outliers start: 20 outliers final: 13 residues processed: 86 average time/residue: 1.0420 time to fit residues: 95.2013 Evaluate side-chains 82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102811 restraints weight = 9515.096| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.30 r_work: 0.3148 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6522 Z= 0.156 Angle : 0.518 8.162 8802 Z= 0.269 Chirality : 0.039 0.144 1014 Planarity : 0.003 0.040 1098 Dihedral : 3.489 15.541 843 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.78 % Allowed : 13.58 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.31), residues: 753 helix: 3.84 (0.27), residues: 309 sheet: 2.98 (0.67), residues: 63 loop : -1.48 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 8 HIS 0.001 0.001 HIS C 124 PHE 0.016 0.001 PHE C 178 TYR 0.007 0.001 TYR C 159 ARG 0.009 0.001 ARG B 141 *********************** 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 93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.823 Fit side-chains REVERT: C 70 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: C 206 LYS cc_start: 0.8874 (tttm) cc_final: 0.8548 (ttpt) REVERT: A 224 ILE cc_start: 0.8311 (mt) cc_final: 0.8045 (mt) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 1.0690 time to fit residues: 94.1459 Evaluate side-chains 74 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 241 LEU 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 45 VAL Chi-restraints excluded: chain B residue 241 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.135796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106125 restraints weight = 9128.083| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.25 r_work: 0.3176 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6522 Z= 0.158 Angle : 0.523 8.446 8802 Z= 0.271 Chirality : 0.039 0.155 1014 Planarity : 0.003 0.027 1098 Dihedral : 3.415 15.179 843 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.61 % Allowed : 14.13 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.31), residues: 753 helix: 3.86 (0.27), residues: 309 sheet: 2.98 (0.67), residues: 63 loop : -1.50 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 8 HIS 0.002 0.001 HIS C 158 PHE 0.015 0.001 PHE C 178 TYR 0.015 0.001 TYR A 228 ARG 0.006 0.000 ARG B 102 *********************** 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 95 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.728 Fit side-chains REVERT: C 206 LYS cc_start: 0.8881 (tttm) cc_final: 0.8552 (ttpt) REVERT: C 226 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (t0) REVERT: A 224 ILE cc_start: 0.8288 (mt) cc_final: 0.8036 (mt) REVERT: B 28 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7204 (tm-30) outliers start: 19 outliers final: 9 residues processed: 85 average time/residue: 1.0798 time to fit residues: 97.4678 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 : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE 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 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 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 5 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 0.0020 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.131826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101839 restraints weight = 9369.924| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.30 r_work: 0.3098 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6522 Z= 0.193 Angle : 0.536 8.791 8802 Z= 0.281 Chirality : 0.040 0.175 1014 Planarity : 0.003 0.046 1098 Dihedral : 3.493 15.232 843 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.16 % Allowed : 13.99 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.31), residues: 753 helix: 3.78 (0.27), residues: 309 sheet: 2.95 (0.67), residues: 63 loop : -1.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 8 HIS 0.002 0.001 HIS A 124 PHE 0.026 0.001 PHE C 178 TYR 0.021 0.001 TYR A 228 ARG 0.012 0.001 ARG B 141 *********************** 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: 23 poor density : 74 time to evaluate : 0.731 Fit side-chains REVERT: C 206 LYS cc_start: 0.8911 (tttm) cc_final: 0.8569 (ttpt) REVERT: A 224 ILE cc_start: 0.8342 (mt) cc_final: 0.8062 (mt) REVERT: B 21 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8311 (mtpp) outliers start: 23 outliers final: 14 residues processed: 89 average time/residue: 1.0466 time to fit residues: 99.0530 Evaluate side-chains 80 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 45 VAL 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 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 62 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 67 optimal weight: 0.0000 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.135223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105819 restraints weight = 9182.179| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.28 r_work: 0.3170 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6522 Z= 0.179 Angle : 0.562 9.116 8802 Z= 0.284 Chirality : 0.040 0.167 1014 Planarity : 0.003 0.029 1098 Dihedral : 3.462 15.531 843 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.74 % Allowed : 14.27 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.31), residues: 753 helix: 3.78 (0.27), residues: 309 sheet: 2.94 (0.68), residues: 63 loop : -1.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 8 HIS 0.002 0.001 HIS C 158 PHE 0.023 0.001 PHE C 178 TYR 0.014 0.001 TYR A 228 ARG 0.006 0.001 ARG B 102 *********************** 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 90 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.704 Fit side-chains REVERT: C 206 LYS cc_start: 0.8883 (tttm) cc_final: 0.8558 (ttpt) REVERT: C 226 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8184 (t0) REVERT: A 224 ILE cc_start: 0.8321 (mt) cc_final: 0.8049 (mt) REVERT: B 8 TRP cc_start: 0.8231 (m100) cc_final: 0.7970 (m100) REVERT: B 21 LYS cc_start: 0.8549 (mmpt) cc_final: 0.8322 (mtpp) REVERT: B 28 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7238 (tm-30) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 1.1892 time to fit residues: 101.9848 Evaluate side-chains 86 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 2 PHE Chi-restraints excluded: chain A residue 45 VAL 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 73 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.131200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101205 restraints weight = 9486.232| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.30 r_work: 0.3084 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2228 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= 0.217 Angle : 0.586 9.976 8802 Z= 0.299 Chirality : 0.040 0.163 1014 Planarity : 0.004 0.053 1098 Dihedral : 3.596 15.820 843 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.61 % Allowed : 14.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.31), residues: 753 helix: 3.70 (0.26), residues: 309 sheet: 2.93 (0.69), residues: 63 loop : -1.60 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 8 HIS 0.003 0.001 HIS C 158 PHE 0.022 0.001 PHE C 178 TYR 0.015 0.001 TYR A 228 ARG 0.014 0.001 ARG B 141 *********************** 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 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.847 Fit side-chains REVERT: C 206 LYS cc_start: 0.8924 (tttm) cc_final: 0.8591 (ttpt) REVERT: C 226 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8164 (t0) REVERT: A 224 ILE cc_start: 0.8384 (mt) cc_final: 0.8125 (mt) REVERT: B 8 TRP cc_start: 0.8255 (m100) cc_final: 0.7982 (m100) outliers start: 19 outliers final: 14 residues processed: 84 average time/residue: 1.1641 time to fit residues: 103.6174 Evaluate side-chains 85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 2 PHE Chi-restraints excluded: chain A residue 45 VAL 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 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 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.132827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102885 restraints weight = 9266.338| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.26 r_work: 0.3127 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6522 Z= 0.252 Angle : 0.604 8.352 8802 Z= 0.306 Chirality : 0.041 0.157 1014 Planarity : 0.003 0.030 1098 Dihedral : 3.691 16.355 843 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.06 % Allowed : 15.23 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.31), residues: 753 helix: 3.60 (0.26), residues: 309 sheet: 2.92 (0.70), residues: 63 loop : -1.65 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 8 HIS 0.003 0.001 HIS C 158 PHE 0.021 0.002 PHE C 178 TYR 0.017 0.001 TYR A 228 ARG 0.006 0.001 ARG B 102 ********************** 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 85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.741 Fit side-chains REVERT: C 206 LYS cc_start: 0.8904 (tttm) cc_final: 0.8574 (ttpt) REVERT: C 226 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8092 (t0) REVERT: A 70 GLU cc_start: 0.7975 (tp30) cc_final: 0.7646 (tm-30) REVERT: A 224 ILE cc_start: 0.8441 (mt) cc_final: 0.8190 (mt) REVERT: B 8 TRP cc_start: 0.8337 (m100) cc_final: 0.8112 (m100) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 1.1268 time to fit residues: 96.6346 Evaluate side-chains 82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 45 VAL 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 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 16 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.132294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102309 restraints weight = 9384.153| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.26 r_work: 0.3097 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6522 Z= 0.272 Angle : 0.623 9.695 8802 Z= 0.317 Chirality : 0.042 0.196 1014 Planarity : 0.004 0.031 1098 Dihedral : 3.769 16.818 843 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.92 % Allowed : 15.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.31), residues: 753 helix: 3.50 (0.27), residues: 309 sheet: 2.90 (0.71), residues: 63 loop : -1.72 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 8 HIS 0.004 0.001 HIS C 158 PHE 0.020 0.002 PHE C 178 TYR 0.019 0.001 TYR A 228 ARG 0.006 0.001 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4357.61 seconds wall clock time: 77 minutes 48.04 seconds (4668.04 seconds total)