Starting phenix.real_space_refine on Mon Jun 9 22:10:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vj9_43277/06_2025/8vj9_43277.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vj9_43277/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vj9_43277/06_2025/8vj9_43277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vj9_43277/06_2025/8vj9_43277.map" model { file = "/net/cci-nas-00/data/ceres_data/8vj9_43277/06_2025/8vj9_43277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vj9_43277/06_2025/8vj9_43277.cif" } resolution = 3.3 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= 0.020 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.36, per 1000 atoms: 0.49 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: 2.82 Conformation dependent library (CDL) restraints added in 793.7 milliseconds 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: 1.05 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: 4.00 Time building geometry restraints manager: 3.28 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: 2.490 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: 0.200 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- 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 : 18.74 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 (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: -2.26 (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 TRP 0.017 0.002 TRP H 50 HIS 0.009 0.001 HIS H 38 PHE 0.015 0.002 PHE A 145 TYR 0.018 0.002 TYR H 36 ARG 0.004 0.001 ARG L 143 Details of bonding type rmsd hydrogen bonds : bond 0.11367 ( 195) hydrogen bonds : angle 7.72609 ( 585) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.69124 ( 8) covalent geometry : bond 0.00591 ( 5630) covalent geometry : angle 0.77276 ( 7636) *********************** 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 : 0.885 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: symmetry clash REVERT: H 37 ILE cc_start: 0.4049 (mm) cc_final: 0.3820 (tp) REVERT: L 140 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6076 (p90) REVERT: L 172 SER cc_start: 0.8694 (m) cc_final: 0.8026 (p) REVERT: A 20 THR cc_start: 0.6007 (m) cc_final: 0.5743 (m) REVERT: A 145 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5914 (m-80) REVERT: A 207 GLU cc_start: 0.3355 (tt0) cc_final: 0.2990 (pm20) REVERT: A 222 THR cc_start: 0.5771 (m) cc_final: 0.5401 (p) REVERT: A 286 ARG cc_start: 0.4484 (mtm180) cc_final: 0.4005 (tmt170) outliers start: 49 outliers final: 30 residues processed: 179 average time/residue: 0.4318 time to fit residues: 96.1914 Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 58 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 32 optimal weight: 0.0020 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4987 r_free = 0.4987 target = 0.223012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.184360 restraints weight = 19381.358| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 3.44 r_work: 0.4465 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.2721 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= 0.138 Angle : 0.582 4.644 7644 Z= 0.304 Chirality : 0.045 0.140 875 Planarity : 0.005 0.042 951 Dihedral : 9.621 81.894 808 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.65 % Allowed : 16.37 % 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 (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 (0.32), residues: 666 helix: -0.38 (0.88), residues: 30 sheet: -0.71 (0.29), residues: 314 loop : -1.85 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 50 HIS 0.008 0.001 HIS A 346 PHE 0.017 0.002 PHE H 141 TYR 0.015 0.001 TYR L 174 ARG 0.007 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 195) hydrogen bonds : angle 6.06437 ( 585) SS BOND : bond 0.00307 ( 4) SS BOND : angle 0.76008 ( 8) covalent geometry : bond 0.00300 ( 5630) covalent geometry : angle 0.58188 ( 7636) *********************** 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 141 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.848 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: 0.4096 (mm) cc_final: 0.3703 (tp) REVERT: L 82 GLU cc_start: 0.5989 (pm20) cc_final: 0.5750 (pm20) REVERT: L 172 SER cc_start: 0.8388 (m) cc_final: 0.7700 (p) REVERT: A 145 PHE cc_start: 0.5892 (OUTLIER) cc_final: 0.5675 (m-80) REVERT: A 207 GLU cc_start: 0.3142 (tt0) cc_final: 0.2810 (pm20) REVERT: A 222 THR cc_start: 0.4606 (m) cc_final: 0.4197 (p) REVERT: A 286 ARG cc_start: 0.4303 (mtm180) cc_final: 0.3488 (tmt170) outliers start: 29 outliers final: 22 residues processed: 137 average time/residue: 0.4134 time to fit residues: 72.0543 Evaluate side-chains 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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 16 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4989 r_free = 0.4989 target = 0.223679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.183839 restraints weight = 19838.040| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 3.59 r_work: 0.4460 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.3174 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= 0.130 Angle : 0.547 4.338 7644 Z= 0.284 Chirality : 0.044 0.138 875 Planarity : 0.005 0.044 951 Dihedral : 8.744 81.668 786 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.37 % Allowed : 18.14 % 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 (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: -1.85 (0.32), residues: 666 helix: -0.65 (0.90), residues: 30 sheet: -0.85 (0.28), residues: 322 loop : -1.61 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.032 0.002 PHE H 141 TYR 0.009 0.001 TYR H 36 ARG 0.003 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 195) hydrogen bonds : angle 5.64565 ( 585) SS BOND : bond 0.00461 ( 4) SS BOND : angle 0.64900 ( 8) covalent geometry : bond 0.00293 ( 5630) covalent geometry : angle 0.54707 ( 7636) *********************** 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 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.863 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: 0.4299 (mm) cc_final: 0.4065 (tp) REVERT: L 82 GLU cc_start: 0.6001 (pm20) cc_final: 0.5788 (pm20) REVERT: L 172 SER cc_start: 0.8420 (m) cc_final: 0.7764 (p) REVERT: L 210 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6743 (m-10) REVERT: L 211 ASN cc_start: 0.7773 (m-40) cc_final: 0.7268 (p0) REVERT: A 207 GLU cc_start: 0.3274 (tt0) cc_final: 0.3027 (pm20) REVERT: A 222 THR cc_start: 0.4650 (m) cc_final: 0.4201 (p) REVERT: A 261 ASP cc_start: 0.5993 (m-30) cc_final: 0.5514 (m-30) REVERT: A 286 ARG cc_start: 0.4357 (mtm180) cc_final: 0.3464 (tmt170) outliers start: 21 outliers final: 18 residues processed: 122 average time/residue: 0.4052 time to fit residues: 63.5718 Evaluate side-chains 118 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 113 SER 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 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 19 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** 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 = 0.4976 r_free = 0.4976 target = 0.221570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.182920 restraints weight = 19452.206| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 3.44 r_work: 0.4446 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.3362 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 : 0.554 4.964 7644 Z= 0.288 Chirality : 0.044 0.138 875 Planarity : 0.005 0.041 951 Dihedral : 8.349 81.283 777 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.17 % Allowed : 17.98 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.84 (0.32), residues: 666 helix: -0.62 (0.90), residues: 30 sheet: -0.66 (0.29), residues: 307 loop : -1.81 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.006 0.001 HIS A 346 PHE 0.014 0.002 PHE A 145 TYR 0.021 0.001 TYR A 48 ARG 0.002 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 195) hydrogen bonds : angle 5.56361 ( 585) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.68961 ( 8) covalent geometry : bond 0.00340 ( 5630) covalent geometry : angle 0.55367 ( 7636) *********************** 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 124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.979 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: 0.4342 (mm) cc_final: 0.4089 (tp) REVERT: L 5 MET cc_start: 0.7306 (mmm) cc_final: 0.7056 (ttm) REVERT: L 82 GLU cc_start: 0.6044 (pm20) cc_final: 0.5818 (pm20) REVERT: L 172 SER cc_start: 0.8461 (m) cc_final: 0.7788 (p) REVERT: L 210 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6734 (m-10) REVERT: L 211 ASN cc_start: 0.7764 (m-40) cc_final: 0.7225 (p0) REVERT: A 207 GLU cc_start: 0.3390 (tt0) cc_final: 0.3118 (pm20) REVERT: A 222 THR cc_start: 0.4637 (m) cc_final: 0.4189 (p) REVERT: A 261 ASP cc_start: 0.6012 (m-30) cc_final: 0.5522 (m-30) REVERT: A 286 ARG cc_start: 0.4505 (mtm180) cc_final: 0.3519 (mpt180) outliers start: 26 outliers final: 23 residues processed: 120 average time/residue: 0.4149 time to fit residues: 63.9950 Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** 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 = 0.4965 r_free = 0.4965 target = 0.221219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.181631 restraints weight = 19882.330| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 3.56 r_work: 0.4427 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.3520 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= 0.153 Angle : 0.549 4.617 7644 Z= 0.286 Chirality : 0.044 0.138 875 Planarity : 0.005 0.041 951 Dihedral : 8.171 81.024 775 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 5.78 % Allowed : 16.69 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.81 (0.32), residues: 666 helix: -0.19 (0.93), residues: 30 sheet: -0.64 (0.29), residues: 307 loop : -1.83 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.014 0.002 PHE A 145 TYR 0.011 0.001 TYR H 36 ARG 0.002 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 195) hydrogen bonds : angle 5.48952 ( 585) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.64916 ( 8) covalent geometry : bond 0.00343 ( 5630) covalent geometry : angle 0.54888 ( 7636) *********************** 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 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.800 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: 0.4314 (mm) cc_final: 0.4044 (tp) REVERT: H 202 THR cc_start: 0.5551 (p) cc_final: 0.5060 (p) REVERT: L 5 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6997 (ttm) REVERT: L 172 SER cc_start: 0.8472 (m) cc_final: 0.7868 (p) REVERT: L 210 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6661 (m-10) REVERT: A 207 GLU cc_start: 0.3488 (tt0) cc_final: 0.3175 (pm20) REVERT: A 222 THR cc_start: 0.4591 (m) cc_final: 0.4140 (p) REVERT: A 261 ASP cc_start: 0.5934 (m-30) cc_final: 0.5550 (m-30) REVERT: A 263 VAL cc_start: 0.5355 (OUTLIER) cc_final: 0.4593 (p) REVERT: A 286 ARG cc_start: 0.4396 (mtm180) cc_final: 0.3373 (mpt180) outliers start: 36 outliers final: 29 residues processed: 126 average time/residue: 0.4058 time to fit residues: 64.5128 Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 20 SER 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 5 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4974 r_free = 0.4974 target = 0.221518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.182702 restraints weight = 19754.714| |-----------------------------------------------------------------------------| r_work (start): 0.4588 rms_B_bonded: 3.48 r_work: 0.4421 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.3767 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= 0.135 Angle : 0.535 4.358 7644 Z= 0.279 Chirality : 0.044 0.134 875 Planarity : 0.004 0.040 951 Dihedral : 8.049 81.055 775 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.62 % Allowed : 16.69 % 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 (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: -1.77 (0.33), residues: 666 helix: 0.06 (0.96), residues: 30 sheet: -0.81 (0.29), residues: 325 loop : -1.61 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.011 0.002 PHE A 62 TYR 0.010 0.001 TYR L 87 ARG 0.002 0.000 ARG L 109 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 195) hydrogen bonds : angle 5.36900 ( 585) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.67225 ( 8) covalent geometry : bond 0.00304 ( 5630) covalent geometry : angle 0.53451 ( 7636) *********************** 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 129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.816 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: 0.4290 (mm) cc_final: 0.4017 (tp) REVERT: H 202 THR cc_start: 0.5301 (p) cc_final: 0.4895 (p) REVERT: L 172 SER cc_start: 0.8420 (m) cc_final: 0.7781 (p) REVERT: L 210 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6605 (m-10) REVERT: A 207 GLU cc_start: 0.3467 (tt0) cc_final: 0.3183 (pm20) REVERT: A 222 THR cc_start: 0.4630 (m) cc_final: 0.4183 (p) REVERT: A 263 VAL cc_start: 0.5366 (OUTLIER) cc_final: 0.4610 (p) REVERT: A 285 LYS cc_start: 0.3422 (mttm) cc_final: 0.3018 (mttt) REVERT: A 286 ARG cc_start: 0.4314 (mtm180) cc_final: 0.3218 (mpt180) outliers start: 35 outliers final: 30 residues processed: 124 average time/residue: 0.3929 time to fit residues: 62.9750 Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 20 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.222163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.183233 restraints weight = 19696.827| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 3.51 r_work: 0.4442 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5634 Z= 0.127 Angle : 0.524 4.300 7644 Z= 0.273 Chirality : 0.044 0.136 875 Planarity : 0.005 0.040 951 Dihedral : 7.942 81.198 775 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.78 % Allowed : 17.66 % 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 (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: -1.73 (0.33), residues: 666 helix: 0.21 (0.99), residues: 30 sheet: -0.81 (0.29), residues: 326 loop : -1.57 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.016 0.002 PHE H 71 TYR 0.009 0.001 TYR L 87 ARG 0.004 0.000 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.02860 ( 195) hydrogen bonds : angle 5.27281 ( 585) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.07549 ( 8) covalent geometry : bond 0.00289 ( 5630) covalent geometry : angle 0.52337 ( 7636) *********************** 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 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.836 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: 0.4227 (mm) cc_final: 0.3965 (tp) REVERT: H 202 THR cc_start: 0.5429 (p) cc_final: 0.5002 (p) REVERT: L 63 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6142 (t80) REVERT: L 172 SER cc_start: 0.8444 (m) cc_final: 0.7796 (p) REVERT: L 210 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: A 207 GLU cc_start: 0.3510 (tt0) cc_final: 0.3171 (pm20) REVERT: A 222 THR cc_start: 0.4520 (m) cc_final: 0.4081 (p) REVERT: A 263 VAL cc_start: 0.5339 (OUTLIER) cc_final: 0.4556 (p) REVERT: A 285 LYS cc_start: 0.3392 (mttm) cc_final: 0.2986 (mttt) REVERT: A 286 ARG cc_start: 0.4243 (mtm180) cc_final: 0.3164 (mpt180) outliers start: 36 outliers final: 31 residues processed: 125 average time/residue: 0.3855 time to fit residues: 62.0152 Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 20 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 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 57 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4975 r_free = 0.4975 target = 0.221805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.181683 restraints weight = 19953.071| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 3.61 r_work: 0.4425 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.4026 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= 0.141 Angle : 0.541 4.471 7644 Z= 0.283 Chirality : 0.044 0.134 875 Planarity : 0.004 0.039 951 Dihedral : 7.911 80.917 775 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 5.78 % Allowed : 17.82 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 (0.33), residues: 666 helix: 0.25 (1.00), residues: 30 sheet: -0.84 (0.29), residues: 326 loop : -1.63 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.012 0.002 PHE A 145 TYR 0.010 0.001 TYR H 36 ARG 0.002 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 195) hydrogen bonds : angle 5.28874 ( 585) SS BOND : bond 0.00252 ( 4) SS BOND : angle 1.66212 ( 8) covalent geometry : bond 0.00320 ( 5630) covalent geometry : angle 0.53813 ( 7636) *********************** 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 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.833 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: 0.4276 (mm) cc_final: 0.4002 (tp) REVERT: H 202 THR cc_start: 0.5491 (p) cc_final: 0.5010 (p) REVERT: L 63 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6226 (t80) REVERT: L 172 SER cc_start: 0.8532 (m) cc_final: 0.7874 (p) REVERT: L 210 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: A 207 GLU cc_start: 0.3560 (tt0) cc_final: 0.3189 (pm20) REVERT: A 222 THR cc_start: 0.4580 (m) cc_final: 0.4129 (p) REVERT: A 263 VAL cc_start: 0.5353 (OUTLIER) cc_final: 0.4582 (p) REVERT: A 285 LYS cc_start: 0.3609 (mttm) cc_final: 0.3213 (mttt) REVERT: A 286 ARG cc_start: 0.4125 (mtm180) cc_final: 0.3086 (mpt180) outliers start: 36 outliers final: 31 residues processed: 125 average time/residue: 0.3907 time to fit residues: 63.4589 Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 20 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 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 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 17 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.4981 r_free = 0.4981 target = 0.222602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.182588 restraints weight = 19998.066| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.62 r_work: 0.4417 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5634 Z= 0.125 Angle : 0.531 4.307 7644 Z= 0.277 Chirality : 0.044 0.137 875 Planarity : 0.004 0.039 951 Dihedral : 7.824 81.071 775 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.46 % Allowed : 17.98 % 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 (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 (0.33), residues: 666 helix: 0.32 (1.00), residues: 30 sheet: -0.66 (0.29), residues: 311 loop : -1.69 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS A 346 PHE 0.011 0.002 PHE L 210 TYR 0.018 0.001 TYR L 56 ARG 0.002 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 195) hydrogen bonds : angle 5.15760 ( 585) SS BOND : bond 0.00114 ( 4) SS BOND : angle 2.15349 ( 8) covalent geometry : bond 0.00285 ( 5630) covalent geometry : angle 0.52710 ( 7636) *********************** 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 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.799 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: 0.4283 (mm) cc_final: 0.4022 (tp) REVERT: H 56 SER cc_start: 0.6587 (OUTLIER) cc_final: 0.5965 (p) REVERT: H 202 THR cc_start: 0.5378 (p) cc_final: 0.4998 (p) REVERT: L 63 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6219 (t80) REVERT: L 172 SER cc_start: 0.8497 (m) cc_final: 0.7859 (p) REVERT: L 210 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: A 207 GLU cc_start: 0.3499 (tt0) cc_final: 0.3050 (pm20) REVERT: A 222 THR cc_start: 0.4555 (m) cc_final: 0.4116 (p) REVERT: A 263 VAL cc_start: 0.5407 (OUTLIER) cc_final: 0.4617 (p) REVERT: A 285 LYS cc_start: 0.3500 (mttm) cc_final: 0.3102 (mttt) REVERT: A 286 ARG cc_start: 0.4120 (mtm180) cc_final: 0.3079 (mpt180) outliers start: 34 outliers final: 30 residues processed: 120 average time/residue: 0.3974 time to fit residues: 61.7758 Evaluate side-chains 124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 20 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 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 129 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4974 r_free = 0.4974 target = 0.221987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.182035 restraints weight = 19924.980| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 3.58 r_work: 0.4406 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5634 Z= 0.136 Angle : 0.548 4.748 7644 Z= 0.286 Chirality : 0.044 0.138 875 Planarity : 0.004 0.039 951 Dihedral : 7.780 80.962 775 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.46 % Allowed : 18.46 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.71 (0.33), residues: 666 helix: 0.35 (1.00), residues: 30 sheet: -0.63 (0.30), residues: 311 loop : -1.76 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.011 0.002 PHE A 145 TYR 0.022 0.001 TYR L 56 ARG 0.002 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 195) hydrogen bonds : angle 5.16755 ( 585) SS BOND : bond 0.00246 ( 4) SS BOND : angle 2.36174 ( 8) covalent geometry : bond 0.00309 ( 5630) covalent geometry : angle 0.54296 ( 7636) ********************** 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: 34 poor density : 92 time to evaluate : 0.842 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: 0.4273 (mm) cc_final: 0.4007 (tp) REVERT: H 56 SER cc_start: 0.6852 (OUTLIER) cc_final: 0.6523 (p) REVERT: H 202 THR cc_start: 0.5436 (p) cc_final: 0.5069 (p) REVERT: L 63 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6307 (t80) REVERT: L 172 SER cc_start: 0.8494 (m) cc_final: 0.7858 (p) REVERT: L 210 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6351 (m-10) REVERT: A 207 GLU cc_start: 0.3555 (tt0) cc_final: 0.3071 (pm20) REVERT: A 222 THR cc_start: 0.4581 (m) cc_final: 0.4138 (p) REVERT: A 263 VAL cc_start: 0.5406 (OUTLIER) cc_final: 0.4628 (p) REVERT: A 285 LYS cc_start: 0.3508 (mttm) cc_final: 0.3119 (mttt) REVERT: A 286 ARG cc_start: 0.4191 (mtm180) cc_final: 0.3118 (mpt180) outliers start: 34 outliers final: 30 residues processed: 121 average time/residue: 0.4024 time to fit residues: 63.5190 Evaluate side-chains 124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 20 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 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 129 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4950 r_free = 0.4950 target = 0.219332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.180748 restraints weight = 19513.575| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 3.42 r_work: 0.4389 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5634 Z= 0.170 Angle : 0.575 5.071 7644 Z= 0.302 Chirality : 0.045 0.143 875 Planarity : 0.005 0.039 951 Dihedral : 7.940 80.947 775 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.62 % Allowed : 18.94 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.80 (0.33), residues: 666 helix: 0.51 (1.02), residues: 29 sheet: -0.55 (0.30), residues: 297 loop : -1.95 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.007 0.001 HIS H 38 PHE 0.015 0.002 PHE A 145 TYR 0.013 0.001 TYR L 37 ARG 0.002 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 195) hydrogen bonds : angle 5.33655 ( 585) SS BOND : bond 0.00137 ( 4) SS BOND : angle 1.72726 ( 8) covalent geometry : bond 0.00389 ( 5630) covalent geometry : angle 0.57303 ( 7636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6727.37 seconds wall clock time: 114 minutes 57.62 seconds (6897.62 seconds total)