Starting phenix.real_space_refine on Wed Sep 17 17:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgw_63074/09_2025/9lgw_63074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgw_63074/09_2025/9lgw_63074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lgw_63074/09_2025/9lgw_63074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgw_63074/09_2025/9lgw_63074.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lgw_63074/09_2025/9lgw_63074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgw_63074/09_2025/9lgw_63074.map" } resolution = 2.7 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= 0.110 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: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 3210 2.51 5 N 837 2.21 5 O 900 1.98 5 H 5083 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 10043 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 6805 Classifications: {'peptide': 413} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 391} Chain breaks: 5 Chain: "B" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 3238 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 3, 'TRANS': 186} Chain breaks: 5 Time building chain proxies: 1.77, per 1000 atoms: 0.18 Number of scatterers: 10043 At special positions: 0 Unit cell: (70.62, 81.32, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 O 900 8.00 N 837 7.00 C 3210 6.00 H 5083 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 150 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 196.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 41.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'A' and resid 50 through 62 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.590A pdb=" N GLN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 173 through 184 removed outlier: 5.341A pdb=" N GLN A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 260 through 280 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.634A pdb=" N ASN A 352 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 353' Processing helix chain 'A' and resid 402 through 417 removed outlier: 3.967A pdb=" N ASP A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 428 through 442 removed outlier: 4.063A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 453 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'B' and resid 31 through 38 removed outlier: 3.740A pdb=" N LYS B 35 " --> pdb=" O HIS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 93 through 117 removed outlier: 3.682A pdb=" N GLN B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU B 114 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.978A pdb=" N ARG B 125 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.717A pdb=" N PHE B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 5.614A pdb=" N LEU A 356 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 397 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 286 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE A 315 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 288 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ALA A 317 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS A 290 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N MET A 208 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE A 289 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N MET A 210 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 230 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.503A pdb=" N ASN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 190 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.769A pdb=" N ILE A 40 " --> pdb=" O ASN A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 101 removed outlier: 6.635A pdb=" N VAL A 46 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 125 " --> pdb=" O GLN A 153 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL A 155 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 127 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 135 through 140 removed outlier: 5.897A pdb=" N TYR B 136 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE B 155 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N CYS B 138 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA B 153 " --> pdb=" O CYS B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.761A pdb=" N THR B 55 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N ILE B 18 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N CYS B 21 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN B 84 " --> pdb=" O CYS B 21 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLU B 23 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N LYS B 82 " --> pdb=" O GLU B 23 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 552 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: 2.32 Time building geometry restraints manager: 1.10 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: 5083 1.03 - 1.23: 5 1.23 - 1.42: 2071 1.42 - 1.62: 2957 1.62 - 1.81: 22 Bond restraints: 10138 Sorted by residual: bond pdb=" N VAL B 2 " pdb=" CA VAL B 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" N VAL B 2 " pdb=" H VAL B 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CB ILE B 207 " pdb=" CG2 ILE B 207 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" C ILE A 190 " pdb=" N VAL A 191 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.29e-02 6.01e+03 1.04e+00 bond pdb=" CG LEU A 409 " pdb=" CD2 LEU A 409 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 ... (remaining 10133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 17012 1.02 - 2.03: 1236 2.03 - 3.05: 83 3.05 - 4.07: 29 4.07 - 5.08: 11 Bond angle restraints: 18371 Sorted by residual: angle pdb=" N VAL A 458 " pdb=" CA VAL A 458 " pdb=" C VAL A 458 " ideal model delta sigma weight residual 112.96 108.48 4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N ILE B 211 " pdb=" CA ILE B 211 " pdb=" C ILE B 211 " ideal model delta sigma weight residual 111.62 108.55 3.07 7.90e-01 1.60e+00 1.51e+01 angle pdb=" N GLU B 48 " pdb=" CA GLU B 48 " pdb=" CB GLU B 48 " ideal model delta sigma weight residual 110.49 114.70 -4.21 1.69e+00 3.50e-01 6.21e+00 angle pdb=" C PHE B 8 " pdb=" N LYS B 9 " pdb=" CA LYS B 9 " ideal model delta sigma weight residual 121.63 116.90 4.73 1.92e+00 2.71e-01 6.06e+00 angle pdb=" CA GLU B 122 " pdb=" CB GLU B 122 " pdb=" CG GLU B 122 " ideal model delta sigma weight residual 114.10 119.02 -4.92 2.00e+00 2.50e-01 6.05e+00 ... (remaining 18366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4310 17.93 - 35.87: 303 35.87 - 53.80: 81 53.80 - 71.73: 25 71.73 - 89.66: 3 Dihedral angle restraints: 4722 sinusoidal: 2602 harmonic: 2120 Sorted by residual: dihedral pdb=" CB CYS B 138 " pdb=" SG CYS B 138 " pdb=" SG CYS B 150 " pdb=" CB CYS B 150 " ideal model delta sinusoidal sigma weight residual -86.00 -142.16 56.16 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 85 " pdb=" CB CYS B 85 " ideal model delta sinusoidal sigma weight residual 93.00 139.08 -46.08 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N LEU A 176 " pdb=" CA LEU A 176 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 4719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 421 0.029 - 0.059: 216 0.059 - 0.088: 59 0.088 - 0.118: 56 0.118 - 0.147: 20 Chirality restraints: 772 Sorted by residual: chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA PRO A 75 " pdb=" N PRO A 75 " pdb=" C PRO A 75 " pdb=" CB PRO A 75 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE B 89 " pdb=" N ILE B 89 " pdb=" C ILE B 89 " pdb=" CB ILE B 89 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 769 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 224 " 0.010 2.00e-02 2.50e+03 9.17e-03 2.52e+00 pdb=" CG TYR A 224 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 224 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 224 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 224 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 224 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 224 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 224 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR A 224 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 224 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 224 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 224 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 187 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 188 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 174 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO A 175 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.020 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 5731 2.43 - 2.97: 23882 2.97 - 3.52: 26584 3.52 - 4.06: 37505 4.06 - 4.60: 54184 Nonbonded interactions: 147886 Sorted by model distance: nonbonded pdb=" HD1 PHE A 61 " pdb=" HD2 TYR A 65 " model vdw 1.890 2.100 nonbonded pdb=" HB3 GLU A 63 " pdb=" HG1 THR A 70 " model vdw 1.892 2.270 nonbonded pdb=" H TYR A 54 " pdb=" HD1 TYR A 54 " model vdw 1.900 2.100 nonbonded pdb=" HE1 PHE A 17 " pdb=" HE3 TRP A 189 " model vdw 1.911 2.100 nonbonded pdb=" HD2 ARG A 238 " pdb="HH11 ARG A 238 " model vdw 1.912 2.270 ... (remaining 147881 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 0.004 0.035 5057 Z= 0.172 Angle : 0.592 5.084 6824 Z= 0.334 Chirality : 0.048 0.147 772 Planarity : 0.004 0.038 851 Dihedral : 14.830 89.664 1914 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.62 % Allowed : 17.33 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.35), residues: 579 helix: 0.04 (0.38), residues: 204 sheet: -0.97 (0.42), residues: 139 loop : -1.08 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 216 TYR 0.026 0.002 TYR A 224 PHE 0.019 0.001 PHE A 314 TRP 0.009 0.002 TRP A 312 HIS 0.005 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5055) covalent geometry : angle 0.59045 ( 6820) SS BOND : bond 0.00439 ( 2) SS BOND : angle 1.60320 ( 4) hydrogen bonds : bond 0.14190 ( 206) hydrogen bonds : angle 7.35504 ( 552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7362 (m-40) REVERT: A 67 LYS cc_start: 0.6883 (ttmt) cc_final: 0.6241 (mmpt) REVERT: A 116 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7693 (mm-40) REVERT: A 136 GLU cc_start: 0.6936 (tp30) cc_final: 0.6669 (tp30) REVERT: A 224 TYR cc_start: 0.7148 (m-80) cc_final: 0.6833 (m-80) REVERT: A 297 ASP cc_start: 0.7631 (m-30) cc_final: 0.7347 (m-30) REVERT: A 442 GLN cc_start: 0.7955 (tt0) cc_final: 0.7711 (tt0) REVERT: B 93 ASN cc_start: 0.7759 (m-40) cc_final: 0.7541 (m-40) REVERT: B 106 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8334 (ttm-80) REVERT: B 202 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7214 (pp20) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 1.1372 time to fit residues: 107.7139 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.191987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167848 restraints weight = 15556.649| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.84 r_work: 0.4000 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5057 Z= 0.132 Angle : 0.523 4.719 6824 Z= 0.283 Chirality : 0.046 0.141 772 Planarity : 0.004 0.038 851 Dihedral : 5.738 45.973 666 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.25 % Allowed : 15.16 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.34), residues: 579 helix: 0.27 (0.38), residues: 199 sheet: -0.99 (0.42), residues: 139 loop : -0.96 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.012 0.001 TYR B 217 PHE 0.016 0.001 PHE A 314 TRP 0.006 0.001 TRP A 189 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5055) covalent geometry : angle 0.52265 ( 6820) SS BOND : bond 0.00293 ( 2) SS BOND : angle 1.17848 ( 4) hydrogen bonds : bond 0.03845 ( 206) hydrogen bonds : angle 6.11309 ( 552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.6994 (ttmt) cc_final: 0.6337 (mmpt) REVERT: A 116 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7641 (mm-40) REVERT: A 216 ARG cc_start: 0.7042 (mmp-170) cc_final: 0.6787 (mmp-170) REVERT: A 442 GLN cc_start: 0.7918 (tt0) cc_final: 0.7666 (tt0) REVERT: B 36 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6282 (tm-30) REVERT: B 106 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8399 (ttm-80) outliers start: 18 outliers final: 7 residues processed: 92 average time/residue: 1.1469 time to fit residues: 110.0821 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.188871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164772 restraints weight = 15845.696| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.84 r_work: 0.3969 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5057 Z= 0.212 Angle : 0.575 5.110 6824 Z= 0.311 Chirality : 0.047 0.152 772 Planarity : 0.005 0.046 851 Dihedral : 5.616 40.678 662 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.61 % Allowed : 14.80 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.34), residues: 579 helix: 0.05 (0.37), residues: 198 sheet: -1.12 (0.41), residues: 139 loop : -1.21 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 90 TYR 0.012 0.002 TYR A 433 PHE 0.024 0.002 PHE A 314 TRP 0.010 0.002 TRP A 189 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 5055) covalent geometry : angle 0.57409 ( 6820) SS BOND : bond 0.00428 ( 2) SS BOND : angle 1.40864 ( 4) hydrogen bonds : bond 0.04059 ( 206) hydrogen bonds : angle 5.97824 ( 552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7000 (ttmt) cc_final: 0.6356 (mmpt) REVERT: A 90 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6995 (ttm-80) REVERT: A 116 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7859 (mm-40) REVERT: A 136 GLU cc_start: 0.7249 (tp30) cc_final: 0.6934 (tp30) REVERT: A 331 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6234 (p0) REVERT: A 387 THR cc_start: 0.7028 (p) cc_final: 0.6730 (t) REVERT: A 439 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7972 (mttt) REVERT: A 442 GLN cc_start: 0.7976 (tt0) cc_final: 0.7746 (tt0) REVERT: B 106 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8392 (ttm110) REVERT: B 202 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6989 (pp20) outliers start: 20 outliers final: 8 residues processed: 101 average time/residue: 1.2344 time to fit residues: 129.4623 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.191438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167305 restraints weight = 15736.408| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.87 r_work: 0.3992 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5057 Z= 0.113 Angle : 0.513 4.234 6824 Z= 0.275 Chirality : 0.046 0.144 772 Planarity : 0.004 0.040 851 Dihedral : 5.264 39.502 662 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.53 % Allowed : 15.70 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.34), residues: 579 helix: 0.41 (0.38), residues: 198 sheet: -1.07 (0.40), residues: 139 loop : -1.12 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.014 0.001 TYR A 224 PHE 0.013 0.001 PHE A 314 TRP 0.004 0.001 TRP A 312 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5055) covalent geometry : angle 0.51248 ( 6820) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.15769 ( 4) hydrogen bonds : bond 0.03351 ( 206) hydrogen bonds : angle 5.68290 ( 552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.6985 (ttmt) cc_final: 0.6300 (mmpt) REVERT: A 116 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7739 (mm110) REVERT: A 135 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7801 (tttp) REVERT: A 136 GLU cc_start: 0.7144 (tp30) cc_final: 0.6896 (tp30) REVERT: A 387 THR cc_start: 0.7042 (p) cc_final: 0.6830 (t) REVERT: A 439 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7965 (mttt) REVERT: A 442 GLN cc_start: 0.7925 (tt0) cc_final: 0.7694 (tt0) REVERT: B 106 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8373 (ttm110) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 1.2524 time to fit residues: 126.0086 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 316 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.192026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167984 restraints weight = 15699.136| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.88 r_work: 0.3999 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5057 Z= 0.116 Angle : 0.506 4.245 6824 Z= 0.270 Chirality : 0.046 0.144 772 Planarity : 0.004 0.040 851 Dihedral : 4.890 28.263 658 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.53 % Allowed : 16.06 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.34), residues: 579 helix: 0.52 (0.38), residues: 198 sheet: -1.04 (0.40), residues: 136 loop : -1.12 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.015 0.001 TYR A 224 PHE 0.014 0.001 PHE A 314 TRP 0.004 0.001 TRP A 189 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5055) covalent geometry : angle 0.50559 ( 6820) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.02176 ( 4) hydrogen bonds : bond 0.03269 ( 206) hydrogen bonds : angle 5.50484 ( 552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7010 (ttmt) cc_final: 0.6337 (mmpt) REVERT: A 116 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7734 (mm110) REVERT: A 135 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7814 (tttp) REVERT: A 136 GLU cc_start: 0.7147 (tp30) cc_final: 0.6908 (tp30) REVERT: A 439 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7973 (mttt) REVERT: A 442 GLN cc_start: 0.7895 (tt0) cc_final: 0.7693 (tt0) REVERT: B 36 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5929 (tm-30) REVERT: B 106 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8378 (ttm110) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 1.1778 time to fit residues: 112.8935 Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.191798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.168121 restraints weight = 15740.462| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.82 r_work: 0.4001 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5057 Z= 0.181 Angle : 0.552 4.911 6824 Z= 0.298 Chirality : 0.047 0.147 772 Planarity : 0.005 0.043 851 Dihedral : 5.088 32.978 657 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.53 % Allowed : 16.25 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.34), residues: 579 helix: 0.39 (0.37), residues: 197 sheet: -1.11 (0.40), residues: 136 loop : -1.25 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 337 TYR 0.016 0.002 TYR B 217 PHE 0.021 0.002 PHE A 314 TRP 0.009 0.002 TRP A 189 HIS 0.005 0.002 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 5055) covalent geometry : angle 0.55161 ( 6820) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.17530 ( 4) hydrogen bonds : bond 0.03559 ( 206) hydrogen bonds : angle 5.57942 ( 552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7045 (ttmt) cc_final: 0.6378 (mmpt) REVERT: A 116 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 135 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7786 (tttp) REVERT: A 136 GLU cc_start: 0.7255 (tp30) cc_final: 0.6987 (tp30) REVERT: A 351 ASN cc_start: 0.6522 (m110) cc_final: 0.6240 (m-40) REVERT: A 439 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7993 (mttt) REVERT: A 442 GLN cc_start: 0.8003 (tt0) cc_final: 0.7788 (tt0) REVERT: B 22 ILE cc_start: 0.7655 (tt) cc_final: 0.7312 (tp) REVERT: B 36 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6045 (tm-30) REVERT: B 106 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8415 (ttm110) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 1.1680 time to fit residues: 103.4925 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.167176 restraints weight = 15642.112| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.81 r_work: 0.3989 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5057 Z= 0.201 Angle : 0.567 4.395 6824 Z= 0.307 Chirality : 0.048 0.154 772 Planarity : 0.005 0.044 851 Dihedral : 5.182 33.721 657 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.71 % Allowed : 16.61 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.33), residues: 579 helix: 0.29 (0.37), residues: 196 sheet: -1.16 (0.40), residues: 135 loop : -1.37 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 90 TYR 0.010 0.002 TYR A 433 PHE 0.023 0.002 PHE A 314 TRP 0.010 0.002 TRP A 189 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 5055) covalent geometry : angle 0.56678 ( 6820) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.20464 ( 4) hydrogen bonds : bond 0.03621 ( 206) hydrogen bonds : angle 5.66641 ( 552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7130 (ttmt) cc_final: 0.6548 (tppt) REVERT: A 116 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8030 (mm-40) REVERT: A 135 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7838 (tttp) REVERT: A 136 GLU cc_start: 0.7283 (tp30) cc_final: 0.7006 (tp30) REVERT: A 224 TYR cc_start: 0.7018 (m-10) cc_final: 0.6729 (m-80) REVERT: A 299 LYS cc_start: 0.6294 (ttpp) cc_final: 0.6058 (ttpt) REVERT: A 439 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7957 (mtpt) REVERT: A 442 GLN cc_start: 0.8011 (tt0) cc_final: 0.7804 (tt0) REVERT: B 22 ILE cc_start: 0.7650 (tt) cc_final: 0.7296 (tp) REVERT: B 36 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6174 (tm-30) REVERT: B 106 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8428 (ttm110) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 1.1354 time to fit residues: 106.4992 Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.193677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170588 restraints weight = 15549.234| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.80 r_work: 0.4026 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5057 Z= 0.111 Angle : 0.514 4.467 6824 Z= 0.276 Chirality : 0.046 0.142 772 Planarity : 0.004 0.043 851 Dihedral : 4.869 28.397 657 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.44 % Allowed : 18.23 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.34), residues: 579 helix: 0.53 (0.38), residues: 198 sheet: -1.05 (0.40), residues: 137 loop : -1.20 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.008 0.001 TYR B 96 PHE 0.014 0.001 PHE A 314 TRP 0.008 0.001 TRP A 312 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5055) covalent geometry : angle 0.51407 ( 6820) SS BOND : bond 0.00199 ( 2) SS BOND : angle 0.92955 ( 4) hydrogen bonds : bond 0.03185 ( 206) hydrogen bonds : angle 5.43086 ( 552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7073 (ttmt) cc_final: 0.6441 (tppt) REVERT: A 116 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7808 (mm110) REVERT: A 135 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7830 (tttp) REVERT: A 136 GLU cc_start: 0.7218 (tp30) cc_final: 0.6948 (tp30) REVERT: A 351 ASN cc_start: 0.6435 (m110) cc_final: 0.6159 (m-40) REVERT: A 439 LYS cc_start: 0.8233 (mmtp) cc_final: 0.8021 (mttt) REVERT: A 442 GLN cc_start: 0.7982 (tt0) cc_final: 0.7777 (tt0) REVERT: B 36 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5953 (tm-30) REVERT: B 106 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8366 (ttm110) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 1.1380 time to fit residues: 94.7574 Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.192314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169030 restraints weight = 15762.436| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.82 r_work: 0.4003 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5057 Z= 0.158 Angle : 0.537 4.642 6824 Z= 0.289 Chirality : 0.047 0.144 772 Planarity : 0.004 0.043 851 Dihedral : 4.983 31.627 657 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.44 % Allowed : 19.13 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.34), residues: 579 helix: 0.54 (0.38), residues: 196 sheet: -1.13 (0.40), residues: 136 loop : -1.18 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.017 0.001 TYR B 217 PHE 0.018 0.001 PHE A 314 TRP 0.012 0.002 TRP A 312 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 5055) covalent geometry : angle 0.53638 ( 6820) SS BOND : bond 0.00321 ( 2) SS BOND : angle 1.08514 ( 4) hydrogen bonds : bond 0.03362 ( 206) hydrogen bonds : angle 5.45413 ( 552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7097 (ttmt) cc_final: 0.6428 (mmpt) REVERT: A 116 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7814 (mm110) REVERT: A 135 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7824 (tttp) REVERT: A 136 GLU cc_start: 0.7254 (tp30) cc_final: 0.6982 (tp30) REVERT: A 299 LYS cc_start: 0.6322 (ttpp) cc_final: 0.6104 (ttpt) REVERT: A 351 ASN cc_start: 0.6479 (m110) cc_final: 0.6192 (m-40) REVERT: A 439 LYS cc_start: 0.8250 (mmtp) cc_final: 0.8007 (mtpt) REVERT: A 442 GLN cc_start: 0.8004 (tt0) cc_final: 0.7780 (tt0) REVERT: B 36 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5978 (tm-30) REVERT: B 106 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8413 (ttm110) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 1.2030 time to fit residues: 102.5519 Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 57 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.193215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.170144 restraints weight = 15578.532| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.80 r_work: 0.4013 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5057 Z= 0.130 Angle : 0.524 4.939 6824 Z= 0.281 Chirality : 0.046 0.144 772 Planarity : 0.004 0.042 851 Dihedral : 4.880 29.630 657 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.26 % Allowed : 19.49 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.34), residues: 579 helix: 0.61 (0.38), residues: 197 sheet: -1.08 (0.40), residues: 136 loop : -1.09 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 90 TYR 0.009 0.001 TYR B 96 PHE 0.016 0.001 PHE A 314 TRP 0.014 0.001 TRP A 312 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5055) covalent geometry : angle 0.52405 ( 6820) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.91618 ( 4) hydrogen bonds : bond 0.03226 ( 206) hydrogen bonds : angle 5.38901 ( 552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7045 (ttmt) cc_final: 0.6447 (tppt) REVERT: A 90 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6936 (ttm-80) REVERT: A 116 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7808 (mm110) REVERT: A 135 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7836 (tttp) REVERT: A 136 GLU cc_start: 0.7213 (tp30) cc_final: 0.6952 (tp30) REVERT: A 351 ASN cc_start: 0.6513 (m110) cc_final: 0.6208 (m-40) REVERT: A 439 LYS cc_start: 0.8248 (mmtp) cc_final: 0.8043 (mttt) REVERT: B 36 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5992 (tm-30) REVERT: B 106 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8424 (ttm110) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 1.1844 time to fit residues: 99.7253 Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.193343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.170350 restraints weight = 15635.434| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.80 r_work: 0.4019 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5057 Z= 0.125 Angle : 0.519 4.960 6824 Z= 0.279 Chirality : 0.046 0.144 772 Planarity : 0.004 0.043 851 Dihedral : 4.832 28.469 657 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.08 % Allowed : 20.04 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.34), residues: 579 helix: 0.68 (0.38), residues: 197 sheet: -1.03 (0.40), residues: 136 loop : -1.06 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.006 0.001 TYR A 433 PHE 0.015 0.001 PHE A 314 TRP 0.017 0.002 TRP A 312 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5055) covalent geometry : angle 0.51901 ( 6820) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.97121 ( 4) hydrogen bonds : bond 0.03188 ( 206) hydrogen bonds : angle 5.33528 ( 552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.61 seconds wall clock time: 73 minutes 6.14 seconds (4386.14 seconds total)