Starting phenix.real_space_refine on Wed Sep 17 20:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vj9_43277/09_2025/8vj9_43277.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vj9_43277/09_2025/8vj9_43277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vj9_43277/09_2025/8vj9_43277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vj9_43277/09_2025/8vj9_43277.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vj9_43277/09_2025/8vj9_43277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vj9_43277/09_2025/8vj9_43277.map" } resolution = 3.3 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= 0.020 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 3512 2.51 5 N 931 2.21 5 O 1045 1.98 5 H 5472 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10983 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3182 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Chain: "L" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3115 Classifications: {'peptide': 204} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "R" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 121 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4565 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 263} Chain breaks: 9 Time building chain proxies: 1.77, per 1000 atoms: 0.16 Number of scatterers: 10983 At special positions: 0 Unit cell: (70.618, 96.968, 113.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 2 15.00 O 1045 8.00 N 931 7.00 C 3512 6.00 H 5472 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 240.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 17 sheets defined 6.2% alpha, 46.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.939A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 204 through 208 removed outlier: 3.580A pdb=" N SER H 207 " --> pdb=" O PRO H 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.677A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.593A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.682A pdb=" N LYS A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 5.742A pdb=" N GLY H 19 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.362A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR H 121 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.362A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 139 through 143 removed outlier: 4.698A pdb=" N ALA H 156 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 203 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLY H 158 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 201 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU H 160 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER H 199 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS H 162 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU H 197 " --> pdb=" O LYS H 162 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER H 196 " --> pdb=" O ALA H 187 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA H 187 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER H 198 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 172 through 173 Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 35 through 39 removed outlier: 3.952A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.460A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AB4, first strand: chain 'A' and resid 28 through 29 removed outlier: 5.965A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 84 through 88 removed outlier: 6.386A pdb=" N VAL A 54 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 144 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 142 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 88 removed outlier: 6.386A pdb=" N VAL A 54 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 144 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 142 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 128 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 288 " --> pdb=" O GLN A 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 184 through 188 Processing sheet with id=AB8, first strand: chain 'A' and resid 253 through 259 removed outlier: 7.556A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 234 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 231 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 585 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: 2.14 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5456 1.03 - 1.23: 38 1.23 - 1.42: 2334 1.42 - 1.62: 3248 1.62 - 1.81: 26 Bond restraints: 11102 Sorted by residual: bond pdb=" CG2 TPO R 352 " pdb="HG23 TPO R 352 " ideal model delta sigma weight residual 0.970 1.092 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB TPO R 352 " pdb=" HB TPO R 352 " ideal model delta sigma weight residual 0.970 1.091 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CB TPO R 355 " pdb=" HB TPO R 355 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CG2 TPO R 355 " pdb="HG21 TPO R 355 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CG2 TPO R 355 " pdb="HG23 TPO R 355 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 ... (remaining 11097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 19950 2.70 - 5.40: 78 5.40 - 8.10: 5 8.10 - 10.79: 1 10.79 - 13.49: 3 Bond angle restraints: 20037 Sorted by residual: angle pdb=" CB TPO R 352 " pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " ideal model delta sigma weight residual 119.31 105.82 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" CB TPO R 355 " pdb=" OG1 TPO R 355 " pdb=" P TPO R 355 " ideal model delta sigma weight residual 119.31 107.03 12.28 3.00e+00 1.11e-01 1.67e+01 angle pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " pdb=" O1P TPO R 352 " ideal model delta sigma weight residual 100.43 111.69 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" OG1 TPO R 355 " pdb=" P TPO R 355 " pdb=" O1P TPO R 355 " ideal model delta sigma weight residual 100.43 109.84 -9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" N VAL H 32 " pdb=" CA VAL H 32 " pdb=" C VAL H 32 " ideal model delta sigma weight residual 113.00 109.28 3.72 1.30e+00 5.92e-01 8.19e+00 ... (remaining 20032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 4758 16.23 - 32.45: 376 32.45 - 48.68: 114 48.68 - 64.90: 41 64.90 - 81.13: 3 Dihedral angle restraints: 5292 sinusoidal: 2847 harmonic: 2445 Sorted by residual: dihedral pdb=" CA ALA H 95 " pdb=" C ALA H 95 " pdb=" N VAL H 96 " pdb=" CA VAL H 96 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP L 171 " pdb=" C ASP L 171 " pdb=" N SER L 172 " pdb=" CA SER L 172 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA MET H 119 " pdb=" C MET H 119 " pdb=" N ASP H 120 " pdb=" CA ASP H 120 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 486 0.029 - 0.059: 240 0.059 - 0.088: 75 0.088 - 0.118: 55 0.118 - 0.147: 19 Chirality restraints: 875 Sorted by residual: chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA VAL H 40 " pdb=" N VAL H 40 " pdb=" C VAL H 40 " pdb=" CB VAL H 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 872 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 167 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.36e+00 pdb=" N PRO H 168 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 220 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO H 221 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 221 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 221 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 45 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 46 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " -0.018 5.00e-02 4.00e+02 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.12: 347 2.12 - 2.74: 20205 2.74 - 3.36: 30139 3.36 - 3.98: 40047 3.98 - 4.60: 61997 Nonbonded interactions: 152735 Sorted by model distance: nonbonded pdb=" OG SER A 127 " pdb=" H LYS A 171 " model vdw 1.494 2.450 nonbonded pdb=" O1P TPO R 352 " pdb=" HZ1 LYS A 12 " model vdw 1.511 2.450 nonbonded pdb=" HE1 TRP H 50 " pdb=" OG SER H 53 " model vdw 1.552 2.450 nonbonded pdb=" OE2 GLU H 9 " pdb=" H CYS H 99 " model vdw 1.557 2.450 nonbonded pdb=" OE1 GLN H 42 " pdb="HE22 GLN L 39 " model vdw 1.563 2.450 ... (remaining 152730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.050 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.940 Find NCS groups from input model: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.006 0.109 5634 Z= 0.287 Angle : 0.773 13.493 7644 Z= 0.403 Chirality : 0.046 0.147 875 Planarity : 0.005 0.046 951 Dihedral : 12.790 81.126 2034 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 7.87 % Allowed : 11.08 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -2.26 (0.32), residues: 666 helix: -0.82 (0.91), residues: 31 sheet: -0.91 (0.28), residues: 325 loop : -2.20 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 143 TYR 0.018 0.002 TYR H 36 PHE 0.015 0.002 PHE A 145 TRP 0.017 0.002 TRP H 50 HIS 0.009 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 5630) covalent geometry : angle 0.77276 ( 7636) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.69124 ( 8) hydrogen bonds : bond 0.11367 ( 195) hydrogen bonds : angle 7.72609 ( 585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4049 (mm) cc_final: 0.3823 (tp) REVERT: L 140 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6075 (p90) REVERT: L 172 SER cc_start: 0.8694 (m) cc_final: 0.8025 (p) REVERT: A 145 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: A 207 GLU cc_start: 0.3355 (tt0) cc_final: 0.2986 (pm20) REVERT: A 222 THR cc_start: 0.5771 (m) cc_final: 0.5404 (p) REVERT: A 286 ARG cc_start: 0.4484 (mtm180) cc_final: 0.4003 (tmt170) outliers start: 49 outliers final: 30 residues processed: 179 average time/residue: 0.2035 time to fit residues: 45.4605 Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 174 ASN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.222524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.183222 restraints weight = 19622.082| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.48 r_work: 0.4423 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5634 Z= 0.146 Angle : 0.588 4.775 7644 Z= 0.308 Chirality : 0.045 0.141 875 Planarity : 0.005 0.042 951 Dihedral : 9.724 81.750 808 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.98 % Allowed : 16.37 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.93 (0.32), residues: 666 helix: -0.51 (0.86), residues: 30 sheet: -0.73 (0.29), residues: 314 loop : -1.89 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 19 TYR 0.015 0.001 TYR L 174 PHE 0.017 0.002 PHE H 141 TRP 0.017 0.002 TRP H 50 HIS 0.008 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5630) covalent geometry : angle 0.58815 ( 7636) SS BOND : bond 0.00295 ( 4) SS BOND : angle 0.76597 ( 8) hydrogen bonds : bond 0.03604 ( 195) hydrogen bonds : angle 6.14440 ( 585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4150 (mm) cc_final: 0.3752 (tp) REVERT: H 213 TYR cc_start: 0.7743 (m-80) cc_final: 0.7483 (m-80) REVERT: L 82 GLU cc_start: 0.6038 (pm20) cc_final: 0.5790 (pm20) REVERT: L 172 SER cc_start: 0.8402 (m) cc_final: 0.7727 (p) REVERT: A 145 PHE cc_start: 0.5927 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: A 207 GLU cc_start: 0.3170 (tt0) cc_final: 0.2835 (pm20) REVERT: A 222 THR cc_start: 0.4648 (m) cc_final: 0.4233 (p) REVERT: A 279 LEU cc_start: 0.4988 (tt) cc_final: 0.4787 (tt) REVERT: A 286 ARG cc_start: 0.4331 (mtm180) cc_final: 0.3530 (tmt170) outliers start: 31 outliers final: 24 residues processed: 133 average time/residue: 0.1916 time to fit residues: 32.4334 Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 167 GLN Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.5012 r_free = 0.5012 target = 0.225683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.186726 restraints weight = 19628.495| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 3.52 r_work: 0.4481 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5634 Z= 0.112 Angle : 0.525 4.326 7644 Z= 0.273 Chirality : 0.044 0.134 875 Planarity : 0.005 0.042 951 Dihedral : 8.891 81.731 787 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.05 % Allowed : 17.98 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.77 (0.32), residues: 666 helix: -0.65 (0.89), residues: 30 sheet: -0.87 (0.28), residues: 329 loop : -1.47 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 19 TYR 0.008 0.001 TYR L 174 PHE 0.031 0.002 PHE H 141 TRP 0.014 0.001 TRP H 50 HIS 0.008 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5630) covalent geometry : angle 0.52463 ( 7636) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.86114 ( 8) hydrogen bonds : bond 0.02940 ( 195) hydrogen bonds : angle 5.51893 ( 585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4226 (mm) cc_final: 0.3637 (tp) REVERT: H 213 TYR cc_start: 0.7714 (m-80) cc_final: 0.7424 (m-80) REVERT: L 82 GLU cc_start: 0.6036 (pm20) cc_final: 0.5822 (pm20) REVERT: L 172 SER cc_start: 0.8379 (m) cc_final: 0.7730 (p) REVERT: L 210 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6696 (m-10) REVERT: L 211 ASN cc_start: 0.7755 (m-40) cc_final: 0.7236 (p0) REVERT: A 207 GLU cc_start: 0.3283 (tt0) cc_final: 0.3050 (pm20) REVERT: A 222 THR cc_start: 0.4694 (m) cc_final: 0.4244 (p) REVERT: A 286 ARG cc_start: 0.4250 (mtm180) cc_final: 0.3321 (tmt170) outliers start: 19 outliers final: 15 residues processed: 119 average time/residue: 0.1866 time to fit residues: 28.5205 Evaluate side-chains 110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.222882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.183477 restraints weight = 19519.414| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 3.49 r_work: 0.4427 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5634 Z= 0.151 Angle : 0.556 4.605 7644 Z= 0.289 Chirality : 0.044 0.139 875 Planarity : 0.005 0.041 951 Dihedral : 8.330 81.390 777 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.69 % Allowed : 17.82 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.81 (0.33), residues: 666 helix: -0.30 (0.91), residues: 30 sheet: -0.84 (0.29), residues: 322 loop : -1.61 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 212 TYR 0.020 0.001 TYR A 48 PHE 0.017 0.002 PHE H 141 TRP 0.012 0.002 TRP H 50 HIS 0.006 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5630) covalent geometry : angle 0.55568 ( 7636) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.68890 ( 8) hydrogen bonds : bond 0.03129 ( 195) hydrogen bonds : angle 5.57266 ( 585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4364 (mm) cc_final: 0.4120 (tp) REVERT: H 124 GLN cc_start: 0.7864 (mt0) cc_final: 0.7607 (mm110) REVERT: L 57 SER cc_start: 0.8247 (t) cc_final: 0.7913 (m) REVERT: L 82 GLU cc_start: 0.6076 (pm20) cc_final: 0.5848 (pm20) REVERT: L 172 SER cc_start: 0.8463 (m) cc_final: 0.7796 (p) REVERT: L 210 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: L 211 ASN cc_start: 0.7680 (m-40) cc_final: 0.7200 (p0) REVERT: A 207 GLU cc_start: 0.3379 (tt0) cc_final: 0.3129 (pm20) REVERT: A 222 THR cc_start: 0.4760 (m) cc_final: 0.4307 (p) REVERT: A 286 ARG cc_start: 0.4461 (mtm180) cc_final: 0.3496 (mpt180) outliers start: 23 outliers final: 21 residues processed: 115 average time/residue: 0.2112 time to fit residues: 30.6694 Evaluate side-chains 116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 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 = 0.4985 r_free = 0.4985 target = 0.222460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.182922 restraints weight = 19515.063| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.52 r_work: 0.4421 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5634 Z= 0.146 Angle : 0.545 4.583 7644 Z= 0.283 Chirality : 0.044 0.137 875 Planarity : 0.005 0.040 951 Dihedral : 8.149 80.973 775 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.82 % Allowed : 17.17 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.77 (0.33), residues: 666 helix: -0.06 (0.96), residues: 30 sheet: -0.74 (0.29), residues: 319 loop : -1.70 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 212 TYR 0.010 0.001 TYR H 36 PHE 0.014 0.002 PHE A 145 TRP 0.013 0.002 TRP H 50 HIS 0.008 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5630) covalent geometry : angle 0.54480 ( 7636) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.69303 ( 8) hydrogen bonds : bond 0.03053 ( 195) hydrogen bonds : angle 5.44960 ( 585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4320 (mm) cc_final: 0.4057 (tp) REVERT: H 202 THR cc_start: 0.5569 (p) cc_final: 0.5067 (p) REVERT: L 82 GLU cc_start: 0.6104 (pm20) cc_final: 0.5897 (pm20) REVERT: L 83 ASP cc_start: 0.7639 (t0) cc_final: 0.7225 (t70) REVERT: L 172 SER cc_start: 0.8463 (m) cc_final: 0.7845 (p) REVERT: L 210 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6668 (m-10) REVERT: L 211 ASN cc_start: 0.7705 (m-40) cc_final: 0.7209 (p0) REVERT: A 207 GLU cc_start: 0.3468 (tt0) cc_final: 0.3179 (pm20) REVERT: A 222 THR cc_start: 0.4649 (m) cc_final: 0.4194 (p) REVERT: A 263 VAL cc_start: 0.5359 (OUTLIER) cc_final: 0.4597 (p) REVERT: A 286 ARG cc_start: 0.4335 (mtm180) cc_final: 0.3284 (mpt180) outliers start: 30 outliers final: 25 residues processed: 122 average time/residue: 0.2127 time to fit residues: 32.4769 Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 39 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.4988 r_free = 0.4988 target = 0.223260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.183818 restraints weight = 19598.635| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 3.51 r_work: 0.4434 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5634 Z= 0.124 Angle : 0.522 4.258 7644 Z= 0.271 Chirality : 0.044 0.135 875 Planarity : 0.004 0.040 951 Dihedral : 8.002 80.971 775 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.98 % Allowed : 17.34 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.68 (0.33), residues: 666 helix: 0.11 (0.98), residues: 30 sheet: -0.75 (0.29), residues: 326 loop : -1.56 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 212 TYR 0.009 0.001 TYR H 36 PHE 0.011 0.002 PHE A 145 TRP 0.012 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5630) covalent geometry : angle 0.52202 ( 7636) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.66600 ( 8) hydrogen bonds : bond 0.02877 ( 195) hydrogen bonds : angle 5.27556 ( 585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4323 (mm) cc_final: 0.4064 (tp) REVERT: H 202 THR cc_start: 0.5432 (p) cc_final: 0.5038 (p) REVERT: L 83 ASP cc_start: 0.7665 (t0) cc_final: 0.7202 (t70) REVERT: L 172 SER cc_start: 0.8442 (m) cc_final: 0.7844 (p) REVERT: L 210 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6506 (m-10) REVERT: L 211 ASN cc_start: 0.7870 (m-40) cc_final: 0.7284 (p0) REVERT: A 63 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7119 (mpt90) REVERT: A 207 GLU cc_start: 0.3460 (tt0) cc_final: 0.3147 (pm20) REVERT: A 222 THR cc_start: 0.4628 (m) cc_final: 0.4163 (p) REVERT: A 285 LYS cc_start: 0.3527 (mttm) cc_final: 0.3184 (mttt) REVERT: A 286 ARG cc_start: 0.4282 (mtm180) cc_final: 0.3233 (mpt180) outliers start: 31 outliers final: 26 residues processed: 119 average time/residue: 0.2123 time to fit residues: 31.6445 Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.4991 r_free = 0.4991 target = 0.223661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.183942 restraints weight = 19458.437| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 3.54 r_work: 0.4435 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5634 Z= 0.125 Angle : 0.525 4.192 7644 Z= 0.273 Chirality : 0.044 0.136 875 Planarity : 0.004 0.040 951 Dihedral : 7.919 81.100 775 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.98 % Allowed : 17.98 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.60 (0.33), residues: 666 helix: 0.23 (0.99), residues: 30 sheet: -0.62 (0.29), residues: 323 loop : -1.60 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 70 TYR 0.009 0.001 TYR H 36 PHE 0.012 0.002 PHE A 145 TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5630) covalent geometry : angle 0.52511 ( 7636) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.63764 ( 8) hydrogen bonds : bond 0.02836 ( 195) hydrogen bonds : angle 5.20285 ( 585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4321 (mm) cc_final: 0.4064 (tp) REVERT: H 202 THR cc_start: 0.5423 (p) cc_final: 0.4984 (p) REVERT: L 63 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.6185 (t80) REVERT: L 83 ASP cc_start: 0.7685 (t0) cc_final: 0.7277 (t70) REVERT: L 172 SER cc_start: 0.8409 (m) cc_final: 0.7755 (p) REVERT: L 210 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6552 (m-10) REVERT: A 63 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7113 (mpt90) REVERT: A 207 GLU cc_start: 0.3499 (tt0) cc_final: 0.3185 (pm20) REVERT: A 222 THR cc_start: 0.4602 (m) cc_final: 0.4161 (p) REVERT: A 263 VAL cc_start: 0.5346 (OUTLIER) cc_final: 0.4571 (p) REVERT: A 285 LYS cc_start: 0.3524 (mttm) cc_final: 0.3176 (mttt) REVERT: A 286 ARG cc_start: 0.4317 (mtm180) cc_final: 0.3225 (mpt180) outliers start: 31 outliers final: 27 residues processed: 118 average time/residue: 0.2046 time to fit residues: 30.3712 Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4984 r_free = 0.4984 target = 0.222682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.182790 restraints weight = 19489.560| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 3.55 r_work: 0.4426 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5634 Z= 0.136 Angle : 0.533 4.449 7644 Z= 0.278 Chirality : 0.044 0.136 875 Planarity : 0.004 0.040 951 Dihedral : 7.848 80.895 775 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.30 % Allowed : 18.14 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.63 (0.33), residues: 666 helix: 0.27 (1.00), residues: 30 sheet: -0.63 (0.29), residues: 323 loop : -1.66 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.010 0.001 TYR H 36 PHE 0.013 0.002 PHE A 145 TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5630) covalent geometry : angle 0.53325 ( 7636) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.65080 ( 8) hydrogen bonds : bond 0.02894 ( 195) hydrogen bonds : angle 5.19566 ( 585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4297 (mm) cc_final: 0.4029 (tp) REVERT: H 202 THR cc_start: 0.5470 (p) cc_final: 0.4983 (p) REVERT: L 63 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6199 (t80) REVERT: L 83 ASP cc_start: 0.7942 (t0) cc_final: 0.7593 (t0) REVERT: L 172 SER cc_start: 0.8468 (m) cc_final: 0.7850 (p) REVERT: L 210 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6363 (m-10) REVERT: A 207 GLU cc_start: 0.3482 (tt0) cc_final: 0.3173 (pm20) REVERT: A 222 THR cc_start: 0.4634 (m) cc_final: 0.4184 (p) REVERT: A 263 VAL cc_start: 0.5385 (OUTLIER) cc_final: 0.4611 (p) REVERT: A 285 LYS cc_start: 0.3569 (mttm) cc_final: 0.3217 (mttt) REVERT: A 286 ARG cc_start: 0.4248 (mtm180) cc_final: 0.3173 (mpt180) outliers start: 33 outliers final: 27 residues processed: 123 average time/residue: 0.1853 time to fit residues: 29.1701 Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 223 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 = 0.4994 r_free = 0.4994 target = 0.223600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.184456 restraints weight = 19216.633| |-----------------------------------------------------------------------------| r_work (start): 0.4606 rms_B_bonded: 3.48 r_work: 0.4440 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5634 Z= 0.122 Angle : 0.522 4.198 7644 Z= 0.272 Chirality : 0.044 0.135 875 Planarity : 0.004 0.040 951 Dihedral : 7.715 81.202 775 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.98 % Allowed : 18.46 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.55 (0.33), residues: 666 helix: 0.31 (1.01), residues: 30 sheet: -0.51 (0.30), residues: 315 loop : -1.66 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 19 TYR 0.009 0.001 TYR H 36 PHE 0.011 0.002 PHE A 145 TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5630) covalent geometry : angle 0.52000 ( 7636) SS BOND : bond 0.00255 ( 4) SS BOND : angle 1.49234 ( 8) hydrogen bonds : bond 0.02752 ( 195) hydrogen bonds : angle 5.07285 ( 585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4300 (mm) cc_final: 0.4036 (tp) REVERT: H 56 SER cc_start: 0.6602 (OUTLIER) cc_final: 0.6034 (p) REVERT: H 202 THR cc_start: 0.5340 (p) cc_final: 0.4955 (p) REVERT: L 63 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.6133 (t80) REVERT: L 83 ASP cc_start: 0.7927 (t0) cc_final: 0.7551 (t0) REVERT: L 172 SER cc_start: 0.8413 (m) cc_final: 0.7800 (p) REVERT: L 210 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6449 (m-10) REVERT: A 207 GLU cc_start: 0.3475 (tt0) cc_final: 0.3166 (pm20) REVERT: A 222 THR cc_start: 0.4490 (m) cc_final: 0.4061 (p) REVERT: A 263 VAL cc_start: 0.5405 (OUTLIER) cc_final: 0.4633 (p) REVERT: A 285 LYS cc_start: 0.3430 (mttm) cc_final: 0.3081 (mttt) REVERT: A 286 ARG cc_start: 0.4135 (mtm180) cc_final: 0.3117 (mpt180) outliers start: 31 outliers final: 27 residues processed: 121 average time/residue: 0.1957 time to fit residues: 30.5055 Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.225075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.184406 restraints weight = 19769.295| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 3.65 r_work: 0.4434 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5634 Z= 0.117 Angle : 0.524 5.317 7644 Z= 0.273 Chirality : 0.044 0.136 875 Planarity : 0.004 0.040 951 Dihedral : 7.552 80.864 775 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.98 % Allowed : 18.78 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.50 (0.33), residues: 666 helix: 0.50 (1.04), residues: 30 sheet: -0.51 (0.29), residues: 321 loop : -1.63 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 19 TYR 0.009 0.001 TYR H 36 PHE 0.011 0.001 PHE L 210 TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5630) covalent geometry : angle 0.51918 ( 7636) SS BOND : bond 0.00198 ( 4) SS BOND : angle 2.30661 ( 8) hydrogen bonds : bond 0.02665 ( 195) hydrogen bonds : angle 5.01289 ( 585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.4278 (mm) cc_final: 0.4022 (tp) REVERT: H 56 SER cc_start: 0.6796 (OUTLIER) cc_final: 0.6483 (p) REVERT: H 202 THR cc_start: 0.5398 (p) cc_final: 0.5017 (p) REVERT: L 63 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.6190 (t80) REVERT: L 83 ASP cc_start: 0.7930 (t0) cc_final: 0.7649 (t0) REVERT: L 172 SER cc_start: 0.8404 (m) cc_final: 0.7795 (p) REVERT: L 210 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6419 (m-10) REVERT: A 150 PHE cc_start: 0.7041 (p90) cc_final: 0.6663 (t80) REVERT: A 207 GLU cc_start: 0.3473 (tt0) cc_final: 0.3164 (pm20) REVERT: A 222 THR cc_start: 0.4476 (m) cc_final: 0.4051 (p) REVERT: A 263 VAL cc_start: 0.5437 (OUTLIER) cc_final: 0.4615 (p) REVERT: A 286 ARG cc_start: 0.4153 (mtm180) cc_final: 0.3123 (mpt180) outliers start: 31 outliers final: 26 residues processed: 121 average time/residue: 0.2059 time to fit residues: 31.3149 Evaluate side-chains 121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4984 r_free = 0.4984 target = 0.222931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.183175 restraints weight = 19503.544| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 3.53 r_work: 0.4424 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5634 Z= 0.138 Angle : 0.549 6.219 7644 Z= 0.286 Chirality : 0.044 0.137 875 Planarity : 0.005 0.040 951 Dihedral : 7.580 81.145 775 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.65 % Allowed : 19.10 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.60 (0.33), residues: 666 helix: 0.47 (1.03), residues: 30 sheet: -0.47 (0.30), residues: 301 loop : -1.77 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 19 TYR 0.010 0.001 TYR H 36 PHE 0.013 0.002 PHE A 145 TRP 0.010 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5630) covalent geometry : angle 0.54249 ( 7636) SS BOND : bond 0.00724 ( 4) SS BOND : angle 2.69682 ( 8) hydrogen bonds : bond 0.02805 ( 195) hydrogen bonds : angle 5.08389 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.41 seconds wall clock time: 60 minutes 13.14 seconds (3613.14 seconds total)