Starting phenix.real_space_refine on Tue May 13 10:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgw_63074/05_2025/9lgw_63074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgw_63074/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lgw_63074/05_2025/9lgw_63074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgw_63074/05_2025/9lgw_63074.map" model { file = "/net/cci-nas-00/data/ceres_data/9lgw_63074/05_2025/9lgw_63074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgw_63074/05_2025/9lgw_63074.cif" } resolution = 2.7 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= 0.110 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.89, per 1000 atoms: 0.49 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: 2.53 Conformation dependent library (CDL) restraints added in 644.0 milliseconds 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: 0.94 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: 3.47 Time building geometry restraints manager: 3.07 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: 0.590 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: 0.160 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.870 Find NCS groups from input model: 0.060 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- 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 (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: -1.08 (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 TRP 0.009 0.002 TRP A 312 HIS 0.005 0.001 HIS A 316 PHE 0.019 0.001 PHE A 314 TYR 0.026 0.002 TYR A 224 ARG 0.007 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.14190 ( 206) hydrogen bonds : angle 7.35504 ( 552) SS BOND : bond 0.00439 ( 2) SS BOND : angle 1.60320 ( 4) covalent geometry : bond 0.00385 ( 5055) covalent geometry : angle 0.59045 ( 6820) *********************** 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 : 0.720 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: 0.6236 (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: 2.4446 time to fit residues: 232.1925 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 : 0.704 ------------------------------------------------------------------------------- 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 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.192342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168187 restraints weight = 15527.582| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.85 r_work: 0.3999 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5057 Z= 0.126 Angle : 0.519 4.681 6824 Z= 0.281 Chirality : 0.046 0.141 772 Planarity : 0.004 0.038 851 Dihedral : 5.718 45.966 666 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.43 % Allowed : 15.34 % 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 (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: -0.89 (0.34), residues: 579 helix: 0.29 (0.38), residues: 199 sheet: -0.98 (0.42), residues: 139 loop : -0.95 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 189 HIS 0.004 0.001 HIS A 316 PHE 0.016 0.001 PHE A 314 TYR 0.014 0.001 TYR B 217 ARG 0.003 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 206) hydrogen bonds : angle 6.09733 ( 552) SS BOND : bond 0.00273 ( 2) SS BOND : angle 1.15934 ( 4) covalent geometry : bond 0.00286 ( 5055) covalent geometry : angle 0.51851 ( 6820) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.6994 (ttmt) cc_final: 0.6321 (mmpt) REVERT: A 116 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7646 (mm-40) REVERT: A 216 ARG cc_start: 0.7056 (mmp-170) cc_final: 0.6800 (mmp-170) REVERT: A 442 GLN cc_start: 0.7918 (tt0) cc_final: 0.7665 (tt0) REVERT: B 36 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6298 (tm-30) REVERT: B 106 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8398 (ttm-80) outliers start: 19 outliers final: 8 residues processed: 93 average time/residue: 2.3086 time to fit residues: 224.3536 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 22 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 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.190286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165885 restraints weight = 15807.909| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.87 r_work: 0.3981 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5057 Z= 0.160 Angle : 0.538 5.016 6824 Z= 0.290 Chirality : 0.047 0.144 772 Planarity : 0.004 0.044 851 Dihedral : 5.391 39.749 662 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.43 % Allowed : 14.80 % 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 (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: -0.99 (0.34), residues: 579 helix: 0.26 (0.37), residues: 199 sheet: -1.05 (0.41), residues: 139 loop : -1.06 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 189 HIS 0.006 0.001 HIS A 316 PHE 0.020 0.001 PHE A 314 TYR 0.012 0.001 TYR A 433 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 206) hydrogen bonds : angle 5.84447 ( 552) SS BOND : bond 0.00353 ( 2) SS BOND : angle 1.25809 ( 4) covalent geometry : bond 0.00372 ( 5055) covalent geometry : angle 0.53729 ( 6820) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7014 (ttmt) cc_final: 0.6351 (mmpt) REVERT: A 90 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.6967 (ttm-80) REVERT: A 116 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7751 (mm110) REVERT: A 136 GLU cc_start: 0.7165 (tp30) cc_final: 0.6877 (tp30) REVERT: A 387 THR cc_start: 0.7132 (p) cc_final: 0.6825 (t) REVERT: A 442 GLN cc_start: 0.7939 (tt0) cc_final: 0.7708 (tt0) REVERT: B 36 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: B 106 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8399 (ttm110) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 2.3000 time to fit residues: 228.1258 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 : 0.617 ------------------------------------------------------------------------------- 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 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 230 MET 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 27 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.0170 chunk 15 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 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 = 0.4311 r_free = 0.4311 target = 0.191672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167311 restraints weight = 15595.864| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.87 r_work: 0.3992 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5057 Z= 0.126 Angle : 0.509 4.307 6824 Z= 0.273 Chirality : 0.046 0.146 772 Planarity : 0.004 0.040 851 Dihedral : 5.252 39.527 662 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.17 % Allowed : 15.70 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.34), residues: 579 helix: 0.46 (0.38), residues: 198 sheet: -1.06 (0.40), residues: 139 loop : -1.07 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 189 HIS 0.005 0.001 HIS A 316 PHE 0.015 0.001 PHE A 314 TYR 0.016 0.001 TYR B 217 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 206) hydrogen bonds : angle 5.64895 ( 552) SS BOND : bond 0.00296 ( 2) SS BOND : angle 1.13283 ( 4) covalent geometry : bond 0.00289 ( 5055) covalent geometry : angle 0.50839 ( 6820) *********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.6964 (ttmt) cc_final: 0.6288 (mmpt) REVERT: A 116 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7753 (mm110) REVERT: A 135 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7802 (tttp) REVERT: A 136 GLU cc_start: 0.7168 (tp30) cc_final: 0.6915 (tp30) REVERT: A 439 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7969 (mttt) REVERT: A 442 GLN cc_start: 0.7921 (tt0) cc_final: 0.7690 (tt0) REVERT: B 36 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5944 (tm-30) REVERT: B 106 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8383 (ttm110) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 2.4875 time to fit residues: 241.1275 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE 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 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 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 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 = 0.4306 r_free = 0.4306 target = 0.191412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.168009 restraints weight = 15687.139| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.82 r_work: 0.3989 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5057 Z= 0.164 Angle : 0.533 4.441 6824 Z= 0.287 Chirality : 0.046 0.145 772 Planarity : 0.004 0.042 851 Dihedral : 5.248 40.159 660 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.71 % Allowed : 15.88 % 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 (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: -0.98 (0.34), residues: 579 helix: 0.41 (0.38), residues: 196 sheet: -1.07 (0.40), residues: 136 loop : -1.15 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 189 HIS 0.004 0.001 HIS A 138 PHE 0.019 0.001 PHE A 314 TYR 0.011 0.001 TYR A 224 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 206) hydrogen bonds : angle 5.65616 ( 552) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.20965 ( 4) covalent geometry : bond 0.00380 ( 5055) covalent geometry : angle 0.53269 ( 6820) *********************** 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7005 (ttmt) cc_final: 0.6356 (mmpt) REVERT: A 116 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7784 (mm110) REVERT: A 136 GLU cc_start: 0.7110 (tp30) cc_final: 0.6837 (tp30) REVERT: A 439 LYS cc_start: 0.8226 (mmtp) cc_final: 0.8006 (mttt) REVERT: A 442 GLN cc_start: 0.7985 (tt0) cc_final: 0.7762 (tt0) REVERT: B 36 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6066 (tm-30) REVERT: B 106 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8347 (ttm110) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 2.3936 time to fit residues: 217.8095 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 : 0.734 ------------------------------------------------------------------------------- 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 264 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.192392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168952 restraints weight = 15729.373| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.83 r_work: 0.4003 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1376 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= 0.136 Angle : 0.521 4.280 6824 Z= 0.279 Chirality : 0.046 0.144 772 Planarity : 0.004 0.041 851 Dihedral : 5.169 39.936 660 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.35 % Allowed : 16.06 % 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 (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: -0.92 (0.34), residues: 579 helix: 0.48 (0.38), residues: 196 sheet: -1.05 (0.40), residues: 136 loop : -1.14 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 189 HIS 0.004 0.001 HIS A 316 PHE 0.016 0.001 PHE A 314 TYR 0.012 0.001 TYR A 224 ARG 0.002 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 206) hydrogen bonds : angle 5.56528 ( 552) SS BOND : bond 0.00290 ( 2) SS BOND : angle 1.10585 ( 4) covalent geometry : bond 0.00314 ( 5055) covalent geometry : angle 0.52069 ( 6820) *********************** 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: 13 poor density : 77 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6372 (mmpt) REVERT: A 116 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7768 (mm110) REVERT: A 135 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7834 (tttp) REVERT: A 136 GLU cc_start: 0.7118 (tp30) cc_final: 0.6875 (tp30) REVERT: A 439 LYS cc_start: 0.8220 (mmtp) cc_final: 0.8000 (mttt) REVERT: A 442 GLN cc_start: 0.7979 (tt0) cc_final: 0.7776 (tt0) REVERT: B 36 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5907 (tm-30) REVERT: B 106 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8343 (ttm110) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 2.2411 time to fit residues: 197.3188 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 53 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 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.192411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.168755 restraints weight = 15759.187| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 1.83 r_work: 0.4002 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1487 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= 0.158 Angle : 0.532 4.279 6824 Z= 0.286 Chirality : 0.046 0.144 772 Planarity : 0.004 0.042 851 Dihedral : 5.234 40.367 660 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.89 % Allowed : 16.06 % 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 (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: -0.99 (0.34), residues: 579 helix: 0.43 (0.38), residues: 196 sheet: -1.06 (0.40), residues: 136 loop : -1.20 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 312 HIS 0.003 0.001 HIS A 138 PHE 0.019 0.001 PHE A 314 TYR 0.009 0.001 TYR A 433 ARG 0.002 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 206) hydrogen bonds : angle 5.57696 ( 552) SS BOND : bond 0.00326 ( 2) SS BOND : angle 1.17238 ( 4) covalent geometry : bond 0.00369 ( 5055) covalent geometry : angle 0.53125 ( 6820) *********************** 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 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7026 (ttmt) cc_final: 0.6406 (tppt) REVERT: A 116 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7763 (mm-40) REVERT: A 135 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7780 (tttp) REVERT: A 136 GLU cc_start: 0.7227 (tp30) cc_final: 0.6962 (tp30) REVERT: A 224 TYR cc_start: 0.6980 (m-10) cc_final: 0.6692 (m-80) REVERT: A 439 LYS cc_start: 0.8262 (mmtp) cc_final: 0.8059 (mttt) REVERT: A 442 GLN cc_start: 0.7990 (tt0) cc_final: 0.7781 (tt0) REVERT: B 36 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: B 106 ARG cc_start: 0.8629 (mtm-85) cc_final: 0.8376 (ttm110) outliers start: 16 outliers final: 8 residues processed: 85 average time/residue: 2.4019 time to fit residues: 213.0887 Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.192447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169196 restraints weight = 15737.618| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.83 r_work: 0.4004 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1588 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= 0.130 Angle : 0.515 4.492 6824 Z= 0.277 Chirality : 0.046 0.144 772 Planarity : 0.004 0.042 851 Dihedral : 5.123 40.075 660 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.81 % Allowed : 17.15 % 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 (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: -0.90 (0.34), residues: 579 helix: 0.54 (0.38), residues: 196 sheet: -1.04 (0.40), residues: 138 loop : -1.16 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 312 HIS 0.003 0.001 HIS A 316 PHE 0.016 0.001 PHE A 314 TYR 0.007 0.001 TYR A 433 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 206) hydrogen bonds : angle 5.50032 ( 552) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.06856 ( 4) covalent geometry : bond 0.00301 ( 5055) covalent geometry : angle 0.51491 ( 6820) *********************** 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 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6422 (tppt) REVERT: A 116 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7758 (mm110) REVERT: A 135 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7829 (tttp) REVERT: A 136 GLU cc_start: 0.7135 (tp30) cc_final: 0.6884 (tp30) REVERT: A 439 LYS cc_start: 0.8215 (mmtp) cc_final: 0.8000 (mttt) REVERT: A 442 GLN cc_start: 0.7983 (tt0) cc_final: 0.7779 (tt0) REVERT: B 106 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8338 (ttm110) outliers start: 10 outliers final: 9 residues processed: 83 average time/residue: 2.3581 time to fit residues: 205.0112 Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 A residue 429 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 18 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.193206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.169681 restraints weight = 15604.946| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.82 r_work: 0.4007 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5057 Z= 0.145 Angle : 0.530 4.680 6824 Z= 0.284 Chirality : 0.046 0.143 772 Planarity : 0.004 0.042 851 Dihedral : 5.149 40.292 660 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.99 % Allowed : 17.69 % 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 (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: -0.87 (0.34), residues: 579 helix: 0.57 (0.38), residues: 195 sheet: -1.04 (0.40), residues: 136 loop : -1.14 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 312 HIS 0.003 0.001 HIS A 138 PHE 0.017 0.001 PHE A 314 TYR 0.018 0.001 TYR B 217 ARG 0.004 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 206) hydrogen bonds : angle 5.49628 ( 552) SS BOND : bond 0.00298 ( 2) SS BOND : angle 1.13167 ( 4) covalent geometry : bond 0.00336 ( 5055) covalent geometry : angle 0.52952 ( 6820) *********************** 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: 11 poor density : 75 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7046 (ttmt) cc_final: 0.6439 (tppt) REVERT: A 90 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.6917 (ttm-80) REVERT: A 116 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7785 (mm-40) REVERT: A 135 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7801 (tttp) REVERT: A 136 GLU cc_start: 0.7223 (tp30) cc_final: 0.6943 (tp30) REVERT: A 140 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7797 (mtpt) REVERT: A 224 TYR cc_start: 0.6927 (m-10) cc_final: 0.6608 (m-80) REVERT: B 36 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5891 (tm-30) REVERT: B 106 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8376 (ttm110) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 2.3747 time to fit residues: 199.0565 Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 A residue 429 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 149 ILE 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 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.194328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.170799 restraints weight = 15717.226| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.83 r_work: 0.4023 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1760 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= 0.120 Angle : 0.515 4.832 6824 Z= 0.276 Chirality : 0.046 0.143 772 Planarity : 0.004 0.041 851 Dihedral : 5.045 39.730 660 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.62 % Allowed : 18.41 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.34), residues: 579 helix: 0.67 (0.38), residues: 195 sheet: -0.99 (0.40), residues: 136 loop : -1.04 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 312 HIS 0.003 0.001 HIS A 316 PHE 0.015 0.001 PHE A 314 TYR 0.006 0.001 TYR B 110 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 206) hydrogen bonds : angle 5.43097 ( 552) SS BOND : bond 0.00237 ( 2) SS BOND : angle 1.01166 ( 4) covalent geometry : bond 0.00279 ( 5055) covalent geometry : angle 0.51448 ( 6820) ********************** 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: 9 poor density : 76 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.7036 (ttmt) cc_final: 0.6399 (mmpt) REVERT: A 90 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.6912 (ttm-80) REVERT: A 116 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7771 (mm-40) REVERT: A 135 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7824 (tttp) REVERT: A 136 GLU cc_start: 0.7228 (tp30) cc_final: 0.6967 (tp30) REVERT: B 36 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: B 106 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8357 (ttm110) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 2.4032 time to fit residues: 201.2033 Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 429 THR Chi-restraints excluded: chain B residue 36 GLU 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 30 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 A 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.192001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.168578 restraints weight = 15693.306| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.82 r_work: 0.4003 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1834 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= 0.182 Angle : 0.555 4.858 6824 Z= 0.299 Chirality : 0.047 0.145 772 Planarity : 0.004 0.042 851 Dihedral : 5.080 40.578 660 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.17 % Allowed : 18.41 % 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 (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: -0.91 (0.34), residues: 579 helix: 0.55 (0.38), residues: 195 sheet: -1.07 (0.40), residues: 137 loop : -1.16 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 312 HIS 0.004 0.001 HIS A 138 PHE 0.021 0.002 PHE A 314 TYR 0.016 0.002 TYR B 217 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 206) hydrogen bonds : angle 5.54806 ( 552) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.15769 ( 4) covalent geometry : bond 0.00423 ( 5055) covalent geometry : angle 0.55492 ( 6820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8396.83 seconds wall clock time: 144 minutes 37.28 seconds (8677.28 seconds total)